Diff of the two buildlogs: -- --- b1/build.log 2025-04-09 09:15:29.518058639 +0000 +++ b2/build.log 2025-04-09 09:44:29.828750856 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue May 12 02:34:36 -12 2026 -I: pbuilder-time-stamp: 1778596476 +I: Current time: Wed Apr 9 23:17:37 +14 2025 +I: pbuilder-time-stamp: 1744190257 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -36,52 +36,84 @@ dpkg-source: info: applying better_enums.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2170739/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4102197/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 9 09:17 /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/4102197/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4102197/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='8f78b897814f483081cb4914d9a2ea5b' - 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='2170739' - PS1='# ' - PS2='> ' + INVOCATION_ID=9d3f5e1132c24161b051a42fb38a1779 + 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=4102197 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.uHArmicn/pbuilderrc_z83O --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.uHArmicn/b1 --logfile b1/build.log rdkit_202503.1-2.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.uHArmicn/pbuilderrc_ua1O --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.uHArmicn/b2 --logfile b2/build.log rdkit_202503.1-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-32-cloud-arm64 #1 SMP Debian 6.1.129-1 (2025-03-06) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-32-cloud-arm64 #1 SMP Debian 6.1.129-1 (2025-03-06) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2170739/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4102197/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -571,7 +603,7 @@ Get: 365 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20250309-1 [8745 kB] Get: 366 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2024.20250309-1 [17.0 MB] Get: 367 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2024.20250309-2 [25.2 MB] -Fetched 398 MB in 3s (122 MB/s) +Fetched 398 MB in 2s (264 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 ... 19943 files and directories currently installed.) @@ -1750,8 +1782,8 @@ Setting up tzdata (2025b-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue May 12 14:36:46 UTC 2026. -Universal Time is now: Tue May 12 14:36:46 UTC 2026. +Local time is now: Wed Apr 9 09:18:39 UTC 2025. +Universal Time is now: Wed Apr 9 09:18:39 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-4.2) ... @@ -1915,11 +1947,6 @@ Setting up pandoc (3.1.11.1+ds-2) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up ssl-cert (1.1.3) ... -hostname: Name or service not known -make-ssl-cert: Could not get FQDN, using 'codethink03-arm64'. -make-ssl-cert: You may want to fix your /etc/hosts and/or DNS setup and run -make-ssl-cert: 'make-ssl-cert generate-default-snakeoil --force-overwrite' -make-ssl-cert: again. Setting up libboost-date-time1.83-dev:arm64 (1.83.0-4.2) ... Setting up shared-mime-info (2.4-5+b2) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... @@ -2139,7 +2166,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202503.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rdkit_202503.1-2_source.changes +I: user script /srv/workspace/pbuilder/4102197/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/4102197/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202503.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rdkit_202503.1-2_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202503.1-2 dpkg-buildpackage: info: source distribution unstable @@ -2325,7 +2356,7 @@ command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (1.4s) +-- Configuring done (1.0s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17 make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' @@ -2339,102 +2370,102 @@ make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/INCHI-API 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -MF CMakeFiles/RDGeneral.dir/versions.cpp.o.d -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/versions.cpp /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,--dependency-file=CMakeFiles/hc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2025.03.1 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2025.03.1 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so -[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o -[ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o -MF CMakeFiles/ga.dir/util/RandomUtil.cpp.o.d -o 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -MF CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o.d -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/LocaleSwitcher.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/ga/IntegerStringChromosomePolicy.cpp [ 2%] Built target hc +[ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/ga/BinaryStringChromosomePolicy.cpp +[ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o -MF CMakeFiles/ga.dir/util/RandomUtil.cpp.o.d -o CMakeFiles/ga.dir/util/RandomUtil.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/util/RandomUtil.cpp [ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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/build/reproducible-path/rdkit-202503.1/External/GA/util/Util.cpp -[ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -MF CMakeFiles/RDGeneral.dir/versions.cpp.o.d -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/versions.cpp [ 2%] Linking CXX static library librdkitCatch.a cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 @@ -2461,286 +2492,293 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 2%] Built target RDGeneral make -f 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2025.03.1 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 6%] Built target logTestsCatch -make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend +[ 7%] Built target SimDivPickers +make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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../../lib/libRDKitSimDivPickers.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 [ 8%] Linking CXX executable testQuery cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SimDivPickers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2025.03.1 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o 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-I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -MF CMakeFiles/cDataStructs.dir/DataStructs.cpp.o.d -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/DataStructs.cpp -[ 11%] Linking CXX executable testRDValue -cd /build/reproducible-path/rdkit-202503.1/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 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 11%] Building CXX object Code/DataStructs/CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -MF CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o.d -o CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/catch_tests.cpp [ 11%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/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 -DrdMetricMatrixCalc_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -MF CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o.d -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp -[ 11%] Linking CXX executable testDict -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 11%] Built target testDict @@ -2765,6 +2803,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/Wrap/MaxMinPicker.cpp +[ 12%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/UniformGrid3D.cpp +[ 12%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/UniformRealValueGrid3D.cpp +[ 12%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -MF CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/GridUtils.cpp [ 12%] Linking CXX executable catchDataStructs cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/catchDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/catchDataStructs.dir/link.d CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -o catchDataStructs ../RDGeneral/librdkitCatch.a ../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -2778,224 +2822,203 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 12%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/InfoBitRanker.cpp -[ 12%] Linking CXX executable testSimDivPickers -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 -/usr/bin/c++ -g 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Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2025.03.1 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -3041,46 +3062,51 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 17%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK 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CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Bond.cpp +[ 17%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/atomic_data.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -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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directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 18%] Built target cDataStructs -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -MF CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o.d -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/Wrap/rdGeometry.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdInfoTheory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o ../../../../lib/libRDKitInfoTheory.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' 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, @@ -3093,18 +3119,23 @@ /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) | ^~~~~~~~~ +[ 18%] Built target rdInfoTheory +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolPickler.cpp /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FindRings.cpp:1292:36: warning: unused parameter 'mol' [-Wunused-parameter] 1292 | void findRingFamilies(const ROMol &mol) { | ~~~~~~~~~~~~~^~~ +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -MF CMakeFiles/GraphMol.dir/AtomIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/AtomIterators.cpp -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -MF CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/BondIterators.cpp /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolPickler.cpp: In function 'void RDKit::streamReadPositiveChar(std::istream&, char&, int)': /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolPickler.cpp:72:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 72 | if (res < 0) { | ~~~~^~~ +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -MF CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/BondIterators.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Aromaticity.cpp [ 18%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so @@ -3162,1235 +3193,1245 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 20%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend +make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend +make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesParse.cpp -[ 21%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Entering 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesParseOps.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGenericGroups_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERICGROUPS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/CIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Digraph.cpp -[ 22%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so -cd /build/reproducible-path/rdkit-202503.1/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 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp +[ 21%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so -[ 23%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 +[ 21%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so +cd /build/reproducible-path/rdkit-202503.1/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 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+/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 23%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Trajectory.cpp -[ 23%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 23%] Built target MolCatalog -[ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesJSONParsers.cpp.o +[ 21%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Trajectory.cpp +[ 21%] Built target MolCatalog make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend -cd /build/reproducible-path/rdkit-202503.1/obj-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 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/CIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Sort.cpp -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp -[ 23%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/SubstructMatch.cpp -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ 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-DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/lex.yysmiles.cpp -[ 25%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script 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Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp +[ 22%] Built target GenericGroups make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake "--color=" -[ 26%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/LinearSearch.cpp -[ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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../../../lib/libRDKitSmilesParse.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SmilesParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o 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+cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 27%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o +[ 24%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesWrite.cpp +[ 25%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 25%] Built target rdChemicalFeatures make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ForceField /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/ForceField.cpp -[ 27%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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../../../lib/libRDKitCIPLabeler.so +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp +[ 25%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 +[ 25%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2025.03.1 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 27%] Built target CIPLabeler -make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend +[ 25%] Built target ShapeHelpers +make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp +[ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 26%] Built target rdMolCatalog +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o +cd 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule3.cpp +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-MF CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraints.cpp +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp [ 27%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdqueries.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 27%] Built target rdqueries +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS 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Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/DistanceConstraint.cpp [ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdqueries.dir/link.d 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/usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 28%] Built target rdqueries -make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend +[ 28%] Built target rdPartialCharges +[ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/BondStretch.cpp +[ 29%] Built target MolInterchange +make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -MF CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o.d -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -MF CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o.d -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesJSONParsers.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesJSONParsers.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesJSONParsers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesJSONParsers.cpp +[ 30%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so +cd 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../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 30%] Built target SubstructMatch +[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK 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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/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/Params.cpp +[ 30%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 30%] Built target rdMolInterchange +[ 30%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/smarts.tab.cpp +/build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/StretchBend.cpp: In function 'std::pair ForceFields::MMFF::Utils::calcStbnForceConstants(const ForceFields::MMFF::MMFFStbn*)': +/build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/StretchBend.cpp:23:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 23 | const MMFFStbn *mmffStbnParams) { + | ^ +[ 30%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2025.03.1 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 28%] Built target SLNParse +[ 30%] Built target ForceField +[ 31%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 31%] 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 +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 Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend +make[4]: Entering directory 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&& /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/queryTestsCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/graphmolIterTest.dir/itertest.cpp.o -MF CMakeFiles/graphmolIterTest.dir/itertest.cpp.o.d -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/itertest.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-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 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -MF CMakeFiles/smaTest1.dir/smatest.cpp.o.d -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/smatest.cpp +[ 32%] Linking CXX executable moliteratorTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 +[ 32%] Linking CXX executable graphmolcpTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterCatalog.cpp +[ 32%] Built target moliteratorTestsCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolcpTest.dir/link.d CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 28%] Built target SubstructMatch +[ 32%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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&& /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 +[ 32%] Built target graphmolcpTest make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -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-202503.1/Code/GraphMol/Subgraphs/test1.cpp -[ 28%] Linking CXX executable graphmolcpTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 -/usr/bin/c++ -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 -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.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 28%] Built target graphmolcpTest +[ 32%] Built target graphmolIterTest make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/AtomPairs.cpp +[ 33%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 34%] Built target testSubgraphs1 -make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend +[ 36%] Built target testPartialCharges +make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu 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Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -MF CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o.d -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/CoordGen/Wrap/rdCoordGen.cpp -[ 35%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && 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/usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 35%] Built target rdShapeHelpers -[ 35%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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-/build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/StretchBend.cpp: In function 'std::pair ForceFields::MMFF::Utils::calcStbnForceConstants(const ForceFields::MMFF::MMFFStbn*)': -/build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/StretchBend.cpp:23:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 23 | const MMFFStbn *mmffStbnParams) { - | ^ -[ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/DepictUtils.cpp -[ 36%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so +[ 40%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/FingerprintUtil.cpp -[ 37%] Linking CXX shared library ../../lib/libRDKitForceField.so -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2025.03.1 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o 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cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdAbbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 37%] 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-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp -[ 37%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ 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-Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatchers.cpp -[ 38%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/MIFDescriptors.cpp +[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/catch_tests.cpp +[ 41%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Fingerprints.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2025.03.1 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 40%] Built target Fingerprints -make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend -make[4]: Entering directory 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/hashfunctions.cpp -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp: In function 'void RDKit::MMFF::Tools::addStretchBend(const RDKit::ROMol&, RDKit::MMFF::MMFFMolProperties*, ForceFields::ForceField*)': -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp:428:68: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 428 | MMFF::Utils::calcStbnForceConstants(&mmffStbnParams); - | ^ -[ 40%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 +[ 41%] Built target Fingerprints make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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-DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FilterCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 40%] Built target FilterCatalog +[ 41%] Linking CXX shared library ../../../lib/libRDKitDepictor.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o.d -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap 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-mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp -[ 41%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDInchiLib.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp -[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script 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Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInteractionFields.so.1.2025.03.1 ../../../lib/libRDKitMolInteractionFields.so.1 ../../../lib/libRDKitMolInteractionFields.so +[ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenterJSONParser.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenterJSONParser.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenterJSONParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/MolFragmenterJSONParser.cpp +[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 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/usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 45%] Built target rdfiltercatalog [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TDTWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/TDTWriter.cpp -[ 45%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeomHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 45%] Built target DistGeomHelpers [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/TplFileParser.cpp [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o @@ -4399,11 +4440,6 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o -MF CMakeFiles/FileParsers.dir/PDBParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/PDBParser.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -MF CMakeFiles/FileParsers.dir/PDBWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/PDBWriter.cpp -[ 46%] Linking CXX shared module ../../../../rdkit/Chem/rdMIF.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMIF.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMIF.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMIF.so CMakeFiles/rdMIF.dir/rdMIF.cpp.o ../../../../lib/libRDKitMolInteractionFields.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 46%] Built target rdMIF [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -MF CMakeFiles/FileParsers.dir/CMLWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/CMLWriter.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o @@ -4416,13 +4452,8 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeWriter.cpp.o -MF CMakeFiles/FileParsers.dir/MaeWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/MaeWriter.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -MF CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o.d -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/ProximityBonds.cpp -[ 46%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SequenceParsers.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfiltercatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 46%] Built target rdfiltercatalog [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SequenceWriters.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o @@ -4443,100 +4474,100 @@ [ 47%] Built target FileParsers make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/CoordGen /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake "--color=" make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/CoordGen /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/CoordGen 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -MF CMakeFiles/hanoiTest.dir/hanoitest.cpp.o.d -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/hanoitest.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build +[ 48%] Building CXX object 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -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-202503.1/Code/GraphMol/resMolSupplierTest.cpp -[ 48%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o +[ 48%] Building CXX object 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -MF CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o.d -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/test-valgrind.cpp [ 48%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/molBundleTest.dir/testMolBundle.cpp.o -MF CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o.d -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/testMolBundle.cpp +[ 48%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/testSGroup.dir/testSGroup.cpp.o -MF CMakeFiles/testSGroup.dir/testSGroup.cpp.o.d -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/testSGroup.cpp -[ 48%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/test-valgrind.dir/test-valgrind.cpp.o -MF CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o.d -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/test-valgrind.cpp [ 48%] Linking CXX executable test-valgrind cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test-valgrind.dir/link.d "CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o" -o test-valgrind ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -4563,11 +4594,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 48%] Building CXX object Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -MF CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o.d -o CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_organometallics.cpp -[ 48%] Linking CXX executable resMolSupplierTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/resMolSupplierTest.dir/link.d CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 48%] Linking CXX executable graphmoltestPicklerGlobalSetting +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.d CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 48%] Built target resMolSupplierTest +[ 48%] Built target graphmoltestPicklerGlobalSetting make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake "--color=" @@ -4576,47 +4607,47 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 48%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -MF CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o.d -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_sgroups.cpp -[ 48%] Linking CXX executable graphmoltestPicklerGlobalSetting -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 -[ 48%] Linking CXX executable testCoordGen -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/External/CoordGen && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 48%] Linking CXX executable hanoiTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 +[ 48%] Linking CXX executable resMolSupplierTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro 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/usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 48%] Built target graphmoltestPicklerGlobalSetting +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hanoiTest.dir/link.d CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 48%] Built target resMolSupplierTest make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend +[ 48%] Built target hanoiTest make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 48%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && 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../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 48%] Built target testCoordGen make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd 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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/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -MF CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o.d -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_adjustquery.cpp [ 49%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/chiralityTestsCatch.dir/catch_chirality.cpp.o -MF CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o.d -o CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_chirality.cpp -[ 49%] Linking CXX executable hanoiTest -cd 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/usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 49%] Built target hanoiTest +[ 49%] Built target testCoordGen make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 49%] Built target testUFFForceField @@ -4641,13 +4672,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 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graphmolSGroupCatch +[ 50%] Built target testSGroup make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake "--color=" @@ -4656,9 +4685,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o cd 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-std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o -MF CMakeFiles/smiTest1.dir/test.cpp.o.d -o CMakeFiles/smiTest1.dir/test.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/test.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSGroup.dir/link.d CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 50%] Linking CXX executable graphmolSGroupCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolSGroupCatch.dir/link.d CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 50%] Built target testSGroup +[ 50%] Built target graphmolSGroupCatch make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/catch_tests.cpp +[ 50%] Linking CXX executable testMMFFForceField +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 [ 50%] Linking CXX executable 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o -MF CMakeFiles/testDepictor.dir/testDepictor.cpp.o.d -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/testDepictor.cpp -[ 50%] Linking CXX executable graphmoltestPickler -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 50%] Linking CXX executable molopsTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molopsTestsCatch.dir/link.txt --verbose=1 [ 50%] Built target graphmoltestPickler +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build.make Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends 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-Wl,--dependency-file=CMakeFiles/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 50%] Linking CXX executable canonTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 +[ 50%] Linking CXX executable molopsTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molopsTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/canonTestsCatch.dir/link.d CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 50%] Built target molopsTestsCatch +[ 50%] 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-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake "--color=" @@ -4732,11 +4765,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -MF CMakeFiles/fileParsersTest1.dir/test1.cpp.o.d -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/test1.cpp -[ 50%] Linking CXX executable canonTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 50%] Built target canonTestsCatch +[ 50%] Built target molopsTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/DependInfo.cmake "--color=" @@ -4745,6 +4776,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -MF CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o.d -o CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testAtropisomers.cpp +[ 50%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MDLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/MDLParser.cpp [ 51%] Linking CXX executable graphmoltestChirality cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestChirality.dir/link.d CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -4758,8 +4791,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -MF CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o.d -o CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testSquiggleDoubleBonds.cpp -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MDLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/MDLParser.cpp [ 52%] Linking CXX executable nontetrahedralCatch cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/nontetrahedralCatch.dir/link.d CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -o nontetrahedralCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -4799,10 +4830,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/DaylightParser.cpp [ 52%] Linking CXX executable testDepictor cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 +[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/DaylightParser.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDepictor.dir/link.d CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Built target testDepictor @@ -4814,11 +4845,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testMolWriter.cpp -[ 52%] Linking CXX executable testMultithreadedMolSupplier -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMultithreadedMolSupplier.dir/link.d CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionPickler.cpp +[ 52%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGeneralFileReader.dir/link.d CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target testMultithreadedMolSupplier +[ 52%] Built target testGeneralFileReader make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake "--color=" @@ -4827,26 +4860,24 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o -MF CMakeFiles/testTplParser.dir/testTpls.cpp.o.d -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testTpls.cpp -[ 52%] Linking CXX executable testGeneralFileReader -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionPickler.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGeneralFileReader.dir/link.d CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +[ 52%] Linking CXX executable graphmolTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 +[ 52%] Linking CXX executable testMultithreadedMolSupplier +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target testGeneralFileReader +[ 52%] Built target graphmolTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake "--color=" +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMultithreadedMolSupplier.dir/link.d CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-aarch64-linux-gnu' +[ 52%] Built target testMultithreadedMolSupplier [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testMol2ToMol.cpp -[ 52%] Linking CXX executable graphmolTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target graphmolTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake "--color=" @@ -4855,13 +4886,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testSequence.cpp -[ 52%] Linking CXX executable testTplParser -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 -[ 52%] Linking CXX executable testMol2ToMol -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testTplParser.dir/link.d CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 52%] Linking CXX executable testSequence +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSequence.dir/link.d CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target testTplParser +[ 52%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" @@ -4870,6 +4899,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp +[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionWriter.cpp +[ 52%] Linking CXX executable testMol2ToMol +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 +[ 52%] Linking CXX executable testTplParser +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMol2ToMol.dir/link.d CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Built target testMol2ToMol @@ -4881,13 +4916,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/file_parsers_catch.cpp -[ 52%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionWriter.cpp -[ 52%] Linking CXX executable testSequence -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSequence.dir/link.d CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testTplParser.dir/link.d CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target testSequence +[ 52%] Built target testTplParser make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake "--color=" @@ -4896,11 +4927,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -MF CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o.d -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testPropertyLists.cpp -[ 52%] Linking CXX executable testExtendedStereoParsing -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testExtendedStereoParsing.dir/link.d CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 52%] Linking CXX executable depictorCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/depictorCatch.dir/link.d CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target testExtendedStereoParsing +[ 52%] Built target depictorCatch make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake "--color=" @@ -4909,11 +4940,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -MF CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o.d -o CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp -[ 52%] Linking CXX executable depictorCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/depictorCatch.dir/link.d CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 52%] Linking CXX executable testMolWriter +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolWriter.dir/link.d CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target depictorCatch +[ 52%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake "--color=" @@ -4922,11 +4953,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -MF CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o.d -o CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp -[ 52%] Linking CXX executable chiralityTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chiralityTestsCatch.dir/link.d CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitCIPLabeler.so.1.2025.03.1 ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 52%] Linking CXX executable testExtendedStereoParsing +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testExtendedStereoParsing.dir/link.d CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 52%] Built target chiralityTestsCatch +[ 52%] Built target testExtendedStereoParsing make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" @@ -4948,39 +4979,39 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -MF CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o.d -o CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/connectTheDots_catch.cpp -[ 53%] Linking CXX executable testMolWriter -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolWriter.dir/link.d CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionDepict.cpp +[ 53%] Linking CXX executable smiTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 +[ 54%] Linking CXX executable smiTest1 +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 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../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 54%] Built target smiTest1 +[ 54%] Built target chiralityTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/atropisomersCatch.dir/DependInfo.cmake "--color=" @@ -4992,9 +5023,9 @@ [ 54%] Linking CXX executable XYZFileParserCatchTest cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/XYZFileParserCatchTest.dir/link.d CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] Built target XYZFileParserCatchTest make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' @@ -5025,16 +5056,16 @@ make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake "--color=" +[ 54%] Linking CXX executable molfileStereoCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/catch_tests.cpp -[ 54%] Linking CXX executable atropisomersCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/atropisomersCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/atropisomersCatch.dir/link.d CMakeFiles/atropisomersCatch.dir/atropisomers_catch.cpp.o -o atropisomersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molfileStereoCatchTest.dir/link.d CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -o molfileStereoCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitCIPLabeler.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 54%] Built target atropisomersCatch +[ 54%] Built target molfileStereoCatchTest make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake "--color=" @@ -5043,60 +5074,60 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -MF CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o.d -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms/testChemTransforms.cpp -[ 54%] Linking CXX executable cdxmlParserCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cdxmlParserCatchTest.dir/link.d CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionUtils.cpp +[ 55%] Linking CXX executable testPropertyLists +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 +[ 55%] Linking CXX executable v2MolSuppliers +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2MolSuppliers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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cdxmlParserCatchTest make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o -MF CMakeFiles/testFragCatalog.dir/test1.cpp.o.d -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/test1.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-aarch64-linux-gnu' -[ 55%] 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-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp -[ 56%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionUtils.cpp [ 56%] Linking CXX executable graphmolMolOpsTest cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -5125,13 +5156,13 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o -MF CMakeFiles/testFingerprints.dir/test1.cpp.o.d -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/test1.cpp [ 56%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp -[ 56%] Linking CXX executable testFragCatalog -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 [ 56%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/MoleculeParser.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFragCatalog.dir/link.d CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 56%] Linking CXX executable filterCatalogTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/filterCatalogTest.dir/link.d CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 56%] Built target testFragCatalog +[ 56%] Built target filterCatalogTest make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake "--color=" @@ -5140,13 +5171,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp -[ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/BCUT.cpp -[ 56%] Linking CXX executable filterCatalogTest -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/filterCatalogTest.dir/link.d CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 56%] Linking CXX executable testFragCatalog +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFragCatalog.dir/link.d CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 56%] Built target filterCatalogTest +[ 56%] Built target testFragCatalog make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake "--color=" @@ -5155,11 +5184,15 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -MF CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o.d -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp -[ 57%] Linking CXX executable fileParsersTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersTest1.dir/link.d CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/BCUT.cpp +[ 57%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionRunner.cpp +[ 57%] Linking CXX executable substructTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructTestCatch.dir/link.d CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 57%] Built target fileParsersTest1 +[ 57%] Built target substructTestCatch make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake "--color=" @@ -5168,13 +5201,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/catch_tests.cpp -[ 57%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionRunner.cpp -[ 57%] Linking CXX executable testMHFPFingerprint -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMHFPFingerprint.dir/link.d CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 57%] Linking CXX executable fileParsersTest1 +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersTest1.dir/link.d CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 57%] Built target testMHFPFingerprint +[ 57%] Built target fileParsersTest1 make -f Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/DependInfo.cmake "--color=" @@ -5183,25 +5214,25 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -MF CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o.d -o CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp -[ 57%] Linking CXX executable substructTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 [ 57%] Linking CXX executable testSubstructMatch cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructTestCatch.dir/link.d CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 57%] Linking CXX executable testMHFPFingerprint +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSubstructMatch.dir/link.d CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 57%] Built target substructTestCatch +[ 57%] Built target testSubstructMatch make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMHFPFingerprint.dir/link.d CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 57%] Built target testMHFPFingerprint [ 57%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o -MF CMakeFiles/testMolTransforms.dir/test1.cpp.o.d -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c 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Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-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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CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/BCUT.cpp: In function 'std::pair RDKit::Descriptors::{anonymous}::BCUT2D(std::unique_ptr >&, const std::vector&)': /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/BCUT.cpp:70:71: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 70 | const std::vector &atom_props) { | ^ -[ 57%] Linking CXX executable chemTransformsTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 57%] Linking CXX executable testChemTransforms +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testChemTransforms.dir/link.d CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 57%] Built target chemTransformsTestCatch +[ 57%] Built target testChemTransforms make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/catch_tests.cpp -[ 57%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 57%] Built target testChemTransforms +[ 57%] Built target chemTransformsTestCatch make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake "--color=" @@ -5254,6 +5285,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp +[ 58%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp [ 58%] Linking CXX executable testMolTransforms cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolTransforms.dir/link.d CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -5267,56 +5300,54 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp -[ 58%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp -[ 58%] Linking CXX executable forceFieldHelpersCatch -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/forceFieldHelpersCatch.dir/link.txt --verbose=1 +[ 58%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/PreprocessRxn.cpp [ 58%] Linking CXX executable fpGenTestCatch cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fpGenTestCatch.dir/link.d CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/forceFieldHelpersCatch.dir/link.d CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -o forceFieldHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 58%] Built target fpGenTestCatch 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-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-aarch64-linux-gnu' +[ 58%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp +[ 58%] Linking CXX executable forceFieldHelpersCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script 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../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 58%] Built target forceFieldHelpersCatch make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make 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directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 58%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp [ 58%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -MF CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o.d -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp -[ 58%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/PreprocessRxn.cpp -[ 58%] Linking CXX executable testMMFFForceFieldHelpersMultiThread -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 [ 58%] Linking CXX executable fileParsersCatchTest cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.d 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../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 58%] Linking CXX executable testMMFFForceFieldHelpersMultiThread +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersCatchTest.dir/link.d CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 58%] Built target testMMFFForceFieldHelpersMultiThread +[ 58%] Linking CXX executable fpTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 +[ 58%] Built target fileParsersCatchTest make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build -[ 58%] Linking CXX executable fpTestCatch make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 [ 58%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/catch_tests.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersCatchTest.dir/link.d CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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-202503.1/Code/GraphMol/Descriptors/MolDescriptors.cpp [ 59%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o cd 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CMakeFiles/testMolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolAlign.dir/link.d CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 59%] Built target testMolAlign make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake "--color=" @@ -5422,11 +5455,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/catch_tests.cpp -[ 60%] Linking CXX executable testShapeHelpers -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 60%] Linking CXX executable molAlignCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molAlignCatchTest.dir/link.d CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -o molAlignCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 60%] Built target testShapeHelpers +[ 60%] Built target molAlignCatchTest make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake "--color=" @@ -5435,11 +5468,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o -MF CMakeFiles/MMPA.dir/MMPA.cpp.o.d -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/MMPA.cpp -[ 60%] Linking CXX executable testUFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testUFFForceFieldHelpers.dir/link.d CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 60%] Linking CXX executable testShapeHelpers +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 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testUFFForceFieldHelpers +[ 60%] 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-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/DependInfo.cmake "--color=" @@ -5448,28 +5481,28 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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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 -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolCatalog.dir/link.d CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 60%] Linking CXX executable testUFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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/build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Lipinski.cpp [ 60%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -MF CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o.d -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory/trajectoryTest.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 60%] Linking CXX executable testMolCatalog +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 +[ 60%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolCatalog.dir/link.d CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 60%] Built target molAlignCatchTest +[ 60%] Built target testMolCatalog make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 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-I/build/reproducible-path/rdkit-202503.1/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/test1.cpp -[ 60%] Linking CXX executable testFeatures -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ 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&& /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/DependInfo.cmake "--color=" @@ -5491,11 +5522,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/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-202503.1/Code/GraphMol/FMCS/Seed.cpp +[ 60%] Linking CXX shared library ../../../lib/libRDKitMMPA.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2025.03.1 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2025.03.1 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 60%] Built target distGeomHelpersCatch +[ 60%] Built target MMPA make -f Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/DependInfo.cmake "--color=" @@ -5517,13 +5553,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolProcessing_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLPROCESSING_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o -MF CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o.d -o CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/MolProcessing.cpp -[ 61%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/CDXMLParser.cpp -[ 61%] Linking CXX executable testDistGeomHelpers -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDistGeomHelpers.dir/link.d CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /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 +[ 61%] Linking CXX executable distGeomHelpersCatch +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 +[ 61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/distGeomHelpersCatch.dir/link.d CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -o distGeomHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 61%] Built target testDistGeomHelpers +[ 61%] Built target distGeomHelpersCatch make -f Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/build.make Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/DependInfo.cmake "--color=" @@ -5532,14 +5568,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/testMIF.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/testMIF.cpp.o -MF CMakeFiles/testMIF.dir/testMIF.cpp.o.d -o CMakeFiles/testMIF.dir/testMIF.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/testMIF.cpp -[ 61%] Linking CXX shared library ../../../lib/libRDKitMMPA.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2025.03.1 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2025.03.1 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so -[ 61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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-Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDistGeomHelpers.dir/link.d CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 61%] Built target MMPA +[ 61%] Built target testDistGeomHelpers make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake "--color=" @@ -5548,11 +5581,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/MMPA_UnitTest.cpp +[ 61%] Linking CXX executable molHashCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 [ 61%] Linking CXX executable trajectoryTest cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryTest.dir/link.d CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molHashCatchTest.dir/link.d CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitMolHash.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 61%] Built target trajectoryTest +[ 61%] Built target molHashCatchTest make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake "--color=" @@ -5561,28 +5596,39 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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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/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-202503.1/Code/GraphMol/FMCS/Seed.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryTest.dir/link.d CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 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../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolProcessing.so.1.2025.03.1 ../../../lib/libRDKitMolProcessing.so.1 ../../../lib/libRDKitMolProcessing.so +[ 61%] Linking CXX executable testAbbreviations +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 make[4]: Leaving directory 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp [ 63%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 63%] Built target rdMolProcessing -[ 64%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem 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CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/AUTOCORR3D.cpp [ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o @@ -5684,10 +5715,10 @@ cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code 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-DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/WHIM.cpp -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -MF CMakeFiles/Descriptors.dir/CoulombMat.cpp.o.d -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/CoulombMat.cpp [ 66%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 +[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 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/usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' @@ -5695,36 +5726,40 @@ make -f Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse/MarvinParser.cpp +[ 68%] Linking CXX shared library ../../../lib/libRDKitFMCS.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2025.03.1 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Metal.cpp +[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/MolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Normalize.cpp +[ 70%] Linking CXX executable testReactionFingerprints +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReactionFingerprints.dir/link.d CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 70%] Built target FMCS +[ 70%] Built target testReactionFingerprints make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake "--color=" @@ -5756,26 +5796,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2D.cpp -[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp -In file included from /usr/include/c++/14/bits/stl_algobase.h:64, - from /usr/include/c++/14/bits/stl_tree.h:63, - from /usr/include/c++/14/map:62, - from /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Dict.h:19, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:16, - from /build/reproducible-path/rdkit-202503.1/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-202503.1/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:770:42: required from here - 770 | 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) - | ^~~~~~~~~ -[ 70%] Linking CXX executable testReactionFingerprints -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReactionFingerprints.dir/link.d CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 70%] Linking CXX executable testEnumeration +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 +[ 70%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testEnumeration.dir/link.d CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 70%] Built target testReactionFingerprints +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/RascalMCES.dir/link.txt --verbose=1 +[ 70%] Built target testEnumeration make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake "--color=" @@ -5784,8 +5811,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -MF CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o.d -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/testFMCS_Unit.cpp -[ 70%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/RascalMCES.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRascalMCES.so.1 -o ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o CMakeFiles/RascalMCES.dir/RascalResult.cpp.o ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1 ../../../lib/libRDKitRascalMCES.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' @@ -5798,11 +5823,39 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 71%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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Linking CXX executable testEnumeration -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -MF CMakeFiles/MolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Validate.cpp +[ 71%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse/MarvinWriter.cpp +[ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202503.1/Code/GraphMol/MolStandardize/Charge.cpp +In file included from /usr/include/c++/14/bits/stl_algobase.h:64, + from /usr/include/c++/14/bits/stl_tree.h:63, + from /usr/include/c++/14/map:62, + from /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Dict.h:19, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:16, + from /build/reproducible-path/rdkit-202503.1/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-202503.1/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:770:42: required from here + 770 | 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%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/MolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Fragment.cpp +[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp +[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp +[ 71%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Descriptors.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2025.03.1 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/BCUT.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp +[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -MF CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o.d -o CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/mces_catch.cpp -[ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp +[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o +cd 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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFMCS.dir/link.d CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp +[ 72%] Linking CXX executable FMCStest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -MF CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o.d -o CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.cpp -[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp -[ 71%] Linking CXX shared library 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-I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMol.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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/usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so -[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 72%] Built target Descriptors +[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake "--color=" @@ -5870,605 +5937,807 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 72%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp +[ 72%] Linking CXX executable testRascalCluster +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 +[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o +cd 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMol.cpp +[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalCluster.dir/link.d CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 72%] Built target rdFMCS +[ 74%] Built target testRascalCluster +[ 74%] Linking CXX executable rxnTestCatch make -f 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Deprotect.cpp -[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 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cmake_link_script CMakeFiles/rdRascalMCES.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdRascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRascalMCES.so CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o ../../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/PositionVariation.cpp -[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/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-202503.1/Code/GraphMol/Descriptors/testPBF.cpp -[ 73%] Linking CXX executable testATF -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -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/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 76%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawShape.cpp +In file included from /usr/include/c++/14/vector:62, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: +In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', + 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-202503.1/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-202503.1/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))); + | ^ +[ 76%] Linking CXX executable testBCUT +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1 +[ 76%] Linking CXX executable testAUTOCORR2D +cd 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -MF CMakeFiles/testMORSE.dir/testMORSE.cpp.o.d -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/testMORSE.cpp -[ 73%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -cd 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/usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 73%] Built target testEEM +[ 76%] Built target testEEM make -f 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o +[ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o -MF CMakeFiles/test3D.dir/test3D.cpp.o.d -o CMakeFiles/test3D.dir/test3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/test3D.cpp -In file included from /usr/include/c++/14/vector:62, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: -In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', - 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-202503.1/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-202503.1/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))); - | ^ -[ 73%] Linking CXX executable testPBF -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPBF.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testPBF.dir/link.d CMakeFiles/testPBF.dir/testPBF.cpp.o -o testPBF ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 76%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2025.03.1 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 73%] Built target testPBF +[ 76%] Built target MolEnumerator make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 74%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o +[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o -MF 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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/usr/lib/aarch64-linux-gnu/libboost_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-202503.1/Code/GraphMol/MolDraw2D/DrawText.h:19, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawText.cpp:13: +/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawText.cpp:165:47: required from here + 165 | tl = mol_draw.getAtomCoords(std::make_pair(tl.x, tl.y)); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1132 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ +[ 77%] Linking CXX executable testRDF +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDF.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRDF.dir/link.d CMakeFiles/testRDF.dir/testRDF.cpp.o -o testRDF ../../../lib/libRDKitDescriptors.so.1.2025.03.1 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -MF CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o.d -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp -In file included from /usr/include/c++/14/bits/stl_algobase.h:64, - from /usr/include/c++/14/string:51, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawText.h:19, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawText.cpp:13: -/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawText.cpp:165:47: required from here - 165 | tl = mol_draw.getAtomCoords(std::make_pair(tl.x, tl.y)); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1132 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ -[ 76%] Linking CXX executable testDescriptors -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E 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+cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCoulombMat.dir/link.d CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 78%] Built target MolEnumerator +[ 80%] Built target testCoulombMat make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 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object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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molFragmentTest ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule3.cpp +[ 85%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD 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CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp +[ 85%] Linking CXX executable molTautomerTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 +[ 85%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -MF CMakeFiles/rdchem.dir/Mol.cpp.o.d -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Mol.cpp +[ 86%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 86%] Built target molTautomerTest make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E 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-shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 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../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 81%] Built target rdmolops +[ 89%] Built target testMolEnumerator make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd 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Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp -[ 81%] Linking CXX executable testMolEnumerator -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMrvToMol.dir/link.d CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -o testMrvToMol ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 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/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake "--color=" +In file included from /usr/include/c++/14/bits/stl_algobase.h:64, + from /usr/include/c++/14/string:51, + from /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Invariant.h:17, + from /build/reproducible-path/rdkit-202503.1/Code/Numerics/Matrix.h:14, + from /build/reproducible-path/rdkit-202503.1/Code/Numerics/SquareMatrix.h:14, + from /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform3D.h:16, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/AlignMolecules.h:14, + from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: +/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here + 643 | oscores.push_back(std::make_pair(rmsd, score)); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1132 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 81%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem 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Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 81%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 91%] Linking CXX executable cxsmilesTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cxsmilesTest.dir/link.d CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 81%] Built target rdMolDescriptors +[ 91%] Built target cxsmilesTest make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 81%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -MF CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o.d -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGenericGroups.dir/link.d CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 81%] Built target testGenericGroups -[ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Atom.cpp.o -MF CMakeFiles/rdchem.dir/Atom.cpp.o.d -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Atom.cpp -In file included from /usr/include/c++/14/bits/stl_algobase.h:64, - from /usr/include/c++/14/string:51, - from /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/Invariant.h:17, - from /build/reproducible-path/rdkit-202503.1/Code/Numerics/Matrix.h:14, - from /build/reproducible-path/rdkit-202503.1/Code/Numerics/SquareMatrix.h:14, - from /build/reproducible-path/rdkit-202503.1/Code/Geometry/Transform3D.h:16, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/AlignMolecules.h:14, - from /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: -/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': -/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here - 643 | oscores.push_back(std::make_pair(rmsd, score)); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1132 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ -[ 81%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Edge.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3906, @@ -6482,16 +6751,6 @@ /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) | ^~~~~~~~~ -[ 82%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp -[ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Bond.cpp.o -MF CMakeFiles/rdchem.dir/Bond.cpp.o.d -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Bond.cpp -[ 82%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -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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Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/Configuration.cpp -[ 82%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp 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, @@ -6539,334 +6798,45 @@ /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 82%] Linking CXX executable testO3AAlign +[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/RingInfo.cpp.o -MF CMakeFiles/rdchem.dir/RingInfo.cpp.o.d -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/RingInfo.cpp +[ 91%] Linking CXX executable testO3AAlign cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testO3AAlign.dir/link.d CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2025.03.1 ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp -[ 82%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o -cd 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp -[ 82%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp -[ 83%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -cd 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Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/PDBWriter.cpp -[ 87%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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/usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 90%] Built target rdmolfiles -make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2025.03.1 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so +[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 91%] Built target ScaffoldNetwork +[ 91%] Built target rdMolAlign make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" @@ -6875,151 +6845,93 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 91%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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/usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp +[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -MF CMakeFiles/rdchem.dir/MolBundle.cpp.o.d -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MolBundle.cpp +[ 91%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/GeneralizedSubstruct.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared 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target GeneralizedSubstruct make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 91%] Built target molTautomerTest -[ 91%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp -[ 91%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdTautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 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../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 91%] Built target rdTautomerQuery -[ 91%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp -[ 91%] Building CXX object 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o -MF CMakeFiles/rdkit.dir/bfp_op.c.o.d -o CMakeFiles/rdkit.dir/bfp_op.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bfp_op.c +[ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o -MF CMakeFiles/rdkit.dir/cache.c.o.d -o CMakeFiles/rdkit.dir/cache.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/cache.c +[ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o -MF CMakeFiles/rdkit.dir/guc.c.o.d -o CMakeFiles/rdkit.dir/guc.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/guc.c +[ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o -MF CMakeFiles/rdkit.dir/low_gist.c.o.d -o CMakeFiles/rdkit.dir/low_gist.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/low_gist.c +[ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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-Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o -MF CMakeFiles/rdkit.dir/rdkit_gist.c.o.d -o CMakeFiles/rdkit.dir/rdkit_gist.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/rdkit_gist.c +[ 94%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so +cd 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o -MF CMakeFiles/rdkit.dir/bfp_gist.c.o.d -o CMakeFiles/rdkit.dir/bfp_gist.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bfp_gist.c +[ 94%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o +cd 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/usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o -MF CMakeFiles/rdkit.dir/bfp_gin.c.o.d -o CMakeFiles/rdkit.dir/bfp_gin.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bfp_gin.c +[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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/usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o -MF CMakeFiles/rdkit.dir/bitstring.c.o.d -o CMakeFiles/rdkit.dir/bitstring.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/bitstring.c -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o -MF CMakeFiles/rdkit.dir/rdkit_io.c.o.d -o CMakeFiles/rdkit.dir/rdkit_io.c.o -c /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/rdkit_io.c -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/catch_tests.cpp -[ 96%] Linking CXX shared library librdkit.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/rdkit.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,librdkit.so -o librdkit.so CMakeFiles/rdkit.dir/adapter.cpp.o CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o CMakeFiles/rdkit.dir/bfp_gin.c.o CMakeFiles/rdkit.dir/bitstring.c.o CMakeFiles/rdkit.dir/rdkit_io.c.o CMakeFiles/rdkit.dir/rxn_op.c.o CMakeFiles/rdkit.dir/sfp_op.c.o -L/build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/lib /usr/lib/aarch64-linux-gnu/libpq.so ../../../lib/libRDKitRDInchiLib.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libinchi.so ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitMolHash.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 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../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/sql /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/sql -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/data /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/data -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/expected make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 96%] Built target rdkit -[ 96%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp -[ 97%] Linking CXX 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'/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 97%] Built target rdMolStandardize [ 97%] Linking CXX shared library ../../../lib/libRDKitSynthonSpaceSearch.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/SynthonSpaceSearch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryCatchTest.dir/link.d CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 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../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSynthonSpaceSearch.so.1 -o ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1 ../../../lib/libRDKitSynthonSpaceSearch.so -[ 97%] Built target rdRGroupDecomposition make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 97%] Built target SynthonSpaceSearch make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/depend @@ -7214,43 +7174,94 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/depend cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu 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+make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build [ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/rascal_search_catch_tests.cpp [ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -MF CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o.d -o CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/Wrap/rdSynthonSpaceSearch.cpp +[ 98%] Building CXX object 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cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryTest.dir/link.d CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 99%] Built target substructLibraryTest -[ 99%] Linking CXX executable testRGroupDecomp -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 99%] Linking CXX executable substructLibraryCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryCatchTest.dir/link.d CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 99%] Built target testRGroupDecomp +[ 99%] Built target substructLibraryCatchTest +[ 99%] Linking CXX executable gaExample +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 +[ 99%] Linking CXX executable testRGroupDecompInternals +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 99%] Built target gaExample +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecompInternals.dir/link.d CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 99%] Built target testRGroupDecompInternals [ 99%] Linking CXX executable testSynthonSpaceRascalSearch cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceRascalSearch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSynthonSpaceRascalSearch.dir/link.d CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -o testSynthonSpaceRascalSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 99%] Built target testSynthonSpaceRascalSearch -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdSynthonSpaceSearch.so -cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSynthonSpaceSearch.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSynthonSpaceSearch.so CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o ../../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' -[ 99%] Built target rdSynthonSpaceSearch [ 99%] Linking CXX executable testSynthonSpaceSubstructureSearch cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.txt --verbose=1 /usr/bin/ld: CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o: in function `CATCH2_INTERNAL_TEST_20()': @@ -7258,11 +7269,31 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.d CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -o testSynthonSpaceSubstructureSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [ 99%] Built target testSynthonSpaceSubstructureSearch +[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdSynthonSpaceSearch.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSynthonSpaceSearch.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSynthonSpaceSearch.so CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o ../../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 +[ 99%] Built target rdSynthonSpaceSearch +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdRGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../../lib/libRDKitga.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 99%] Built target rdRGroupDecomposition +[ 99%] Linking CXX executable rgroupCatchTests +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rgroupCatchTests.dir/link.d CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[ 99%] Built target rgroupCatchTests [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' [100%] Built target rdSubstructLibrary +[100%] Linking CXX executable testRGroupDecomp +cd /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' +[100%] Built target testRGroupDecomp make[3]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' @@ -12926,7 +12957,7 @@ resolving references... /build/reproducible-path/rdkit-202503.1/Docs/Book/GettingStartedWithContributing.md:273: WARNING: 'myst' cross-reference target not found: 'building-rdkit-for-development' [myst.xref_missing] -WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NameResolutionError(": Failed to resolve 'img.shields.io' ([Errno -3] Temporary failure in name resolution)"))] +WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NameResolutionError(": Failed to resolve 'img.shields.io' ([Errno -3] Temporary failure in name resolution)"))] processing RDKit.tex: done writing... done copying images... [ 1%] images/Cc1ccccc1.png @@ -15600,6 +15631,320 @@ 1: 2 5 1 0 1: M END 1: +3: [23:38:02] Testing Github940: property dictionaries leaking memory +3: [23:38:02] done +3: Testing RDValue +3: Testing RDAny +3: dict set int vect +3: dict get int vect +3: static boost any:0.000219 s +3: dynamic boost any:0.001035 s +3: static RDAny:0.000126 s +3: dynamic RDAny:0.00101 s +3: static RDValue:0 s +3: dynamic RDValue:0.000155 s +3: deleted! +3: [23:38:02] ------------------------------------- +3: [23:38:02] Testing String Pickle Roundtrips. +3: [23:38:02] done +3: [23:38:02] ------------------------------------- +3: [23:38:02] Testing conversion of vect to string. +3: [23:38:02] done +3: [23:38:02] ------------------------------------- +3: [23:38:02] Testing returning const references. +3: [23:38:02] any cast +3: [23:38:02] done: 0.000822 300000 +3: [23:38:02] copy +3: [23:38:02] done: 0.000838 300000 +3: [23:38:02] ref +3: [23:38:02] done: 0.000824 300000 +3: [23:38:02] dict +3: [23:38:02] done: 0.001956 300000 +3: [23:38:02] ref with hasVal +3: [23:38:02] done: 0.001304 300000 +3: [23:38:02] done +3: [23:38:02] ------------------------------------- +3: [23:38:02] Testing dict update. +3: [23:38:02] 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: [23:38:02] +5: ----------------------------------------- +5: [23:38:02] Finished: testPushAndPop() +5: [23:38:02] +5: ----------------------------------------- +5: [23:38:02] +5: ----------------------------------------- +6: Randomness seeded to: 2304148020 +6: =============================================================================== +6: All tests passed (32 assertions in 2 test cases) +6: +7: [23:38:02] should not be silent +7: [23:38:02] should not be silent +7: Randomness seeded to: 1400927798 +7: [23:38:02] should not be silent +7: [23:38:02] should not be silent +7: [23:38:02] should not be silent +7: [23:38:02] should not be silent +7: [23:38:02] should not be silent +7: [23:38:02] should not be silent +7: [23:38:02] should not be silent +7: [23:38:02] should not be silent +7: =============================================================================== +7: All tests passed (26 assertions in 3 test cases) +7: +8: [23:38:02] pass +8: [23:38:02] v3 4 +8: [23:38:02] v4 5 +8: [23:38:02] SPARSE ----------------------------------- +8: [23:38:02] Set 10: 0 +8: [23:38:02] Set 11: 0 +8: [23:38:02] Set 14: 0 +8: [23:38:02] Set 10: 1 +8: [23:38:02] Get 14: 1 +8: [23:38:02] Num: 20 +8: [23:38:02] NumOn: 3 +8: [23:38:02] NumOff: 17 +8: 10, 11, 14, +8: [23:38:02] t2[19]: 0 +8: [23:38:02] t2[14]: 1 +8: [23:38:02] t2[19]: 0 +8: [23:38:02] 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: [23:38:02] Explicit ---------------------------------- +8: [23:38:02] Set 10: 0 +8: [23:38:02] Set 11: 0 +8: [23:38:02] Set 14: 0 +8: [23:38:02] Set 10: 1 +8: [23:38:02] Get 14: 1 +8: [23:38:02] Num: 20 +8: [23:38:02] NumOn: 3 +8: [23:38:02] NumOff: 17 +8: 10, 11, 14, +8: [23:38:02] t2[19]: 0 +8: [23:38:02] t2[14]: 1 +8: [23:38:02] t2[19]: 0 +8: [23:38:02] 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: [23:38:02] Done +8: [23:38:02] Test DiscreteValue Vectors 1 ---------------------------- +8: [23:38:02] Expected failure: Value out of range +8: [23:38:02] Expected failure: Value out of range +8: [23:38:02] Expected failure: Value out of range +8: [23:38:02] Expected failure: Value out of range +8: [23:38:02] Expected failure: Value out of range +8: [23:38:02] Test DiscreteValue Vectors 2 ------------------------------ +8: [23:38:02] Test DiscreteValue Vectors 3 --------------------------- +8: [23:38:02] Test DiscreteValue Operations ----------------------------- +8: [23:38:02] Test DiscreteValue Operations 2 -------------------------- +8: [23:38:02] Test SparseIntVect ------------------------------------ +8: [23:38:02] Test SparseIntVect Serialization -------------------------- +8: [23:38:02] Test BitVect Serialization ------------------------------- +8: [23:38:02] Test BitVect to FPS ------------------------------- +8: [23:38:02] Test BitVect to binary string ------------------------------- +8: [23:38:02] Test Similarity Measures BitVect ------------------------------- +8: [23:38:02] Test Similarity Measures SparseBitVect ------------------------------- +8: [23:38:02] Test BitVect with all ones ------------------------------- +8: [23:38:02] Test Explicit BitVects: Concatenation Operation ------------------------------- +8: [23:38:02] Test bitmap operations ------------------------------- +8: [23:38:02] Test bitmaps as properties ------------------------------- +8: [23:38:02] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- +8: [23:38:02] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- +8: [23:38:02] Test RealValue Vectors 2: L1Norm ------------------------------- +8: [23:38:02] Test RealValue Vectors 3: Pickles ------------------------------- +8: [23:38:02] Test RealValue Vectors 4: Vector Operations ------------------------------- +11: Randomness seeded to: 3493830397 +11: =============================================================================== +11: All tests passed (3 assertions in 1 test case) +11: + 1/236 Test #3: testDict ............................... Passed 0.13 sec + 2/236 Test #4: testRDValue ............................ Passed 0.12 sec + 3/236 Test #6: dictTestsCatch ......................... Passed 0.09 sec + 4/236 Test #7: logTestsCatch .......................... Passed 0.08 sec + 5/236 Test #8: testDataStructs ........................ Passed 0.06 sec + 6/236 Test #9: testFPB ................................ Passed 0.05 sec + 7/236 Test #11: catchDataStructs ....................... Passed 0.03 sec +test 13 + Start 13: pyDiscreteValueVect + +13: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testDiscreteValueVect.py" +13: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap +13: Test timeout computed to be: 1500 +test 14 + Start 14: pyRealValueVect + +14: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testRealValueVect.py" +14: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap +14: Test timeout computed to be: 1500 +test 15 + Start 15: pySparseIntVect + +15: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testSparseIntVect.py" +15: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap +15: Test timeout computed to be: 1500 +test 16 + Start 16: pyFPB + +16: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testFPB.py" +16: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap +16: Test timeout computed to be: 1500 +test 17 + Start 17: testTransforms + +17: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/testTransforms +17: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry +17: Test timeout computed to be: 1500 +test 18 + Start 18: testGrid + +18: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/testGrid +18: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry +18: Test timeout computed to be: 1500 +test 19 + Start 19: testRealValueGrid + +19: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/testRealValueGrid +19: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry +19: Test timeout computed to be: 1500 +17: **************************************** +17: testPointND +17: **************************************** +17: testPointOps3D +17: **************************************** +17: testPointOps2D +17: **************************************** +17: test12D +17: ref1: 1.01662 3.18622 ref2: 2.40308 3.02108 +17: pt1: 4.32838 4.54621 pt2: 3.37842 3.16057 +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: **************************************** + 8/236 Test #17: testTransforms ......................... Passed 0.04 sec +test 20 + Start 20: geometryTestsCatch + +20: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/geometryTestsCatch +20: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry +20: Test timeout computed to be: 1500 +18: *********************************************************** +18: Testing Grid +18: --------------------------------- +18: testUniformGrid1 +18: +18: --------------------------------- +18: testUniformGrid2 +18: +18: --------------------------------- +18: testUniformGridPickling +18: +18: --------------------------------- +18: testGridOps +18: +18: --------------------------------- +18: testUniformGridIndexing +18: + 9/236 Test #10: testMultiFPB ........................... Passed 0.15 sec + 10/236 Test #18: testGrid ............................... Passed 0.05 sec +test 21 + Start 21: testPyGeometry + +21: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/Geometry/Wrap/testGeometry.py" +21: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/Wrap +21: Test timeout computed to be: 1500 +test 22 + Start 22: testMatrices + +22: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/testMatrices +22: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics +22: Test timeout computed to be: 1500 +20: Randomness seeded to: 3045336170 +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: [23:38:02] ----------------------------------------- +22: [23:38:02] Testing RDNumerics: vectors and matrices Code +22: [23:38:02] --------------------------------------- +22: [23:38:02] test1Vector +22: [23:38:02] --------------------------------------- +22: [23:38:02] test2Matrix +22: [23:38:02] --------------------------------------- +22: [23:38:02] test3SquareMatrix +22: [23:38:02] --------------------------------------- +22: [23:38:02] test4SymmMatrix + 11/236 Test #19: testRealValueGrid ...................... Passed 0.08 sec + 12/236 Test #20: geometryTestsCatch ..................... Passed 0.06 sec + 13/236 Test #22: testMatrices ........................... Passed 0.02 sec +test 23 + Start 23: testConrec + +23: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/testConrec +23: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics +23: Test timeout computed to be: 1500 +test 24 + Start 24: testAlignment + +24: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment +24: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment +24: Test timeout computed to be: 1500 +test 25 + Start 25: pyAlignment + +25: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/Wrap/testAlignment.py" +25: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap +25: Test timeout computed to be: 1500 1: cyclosporine a 1: RDKit 2D 1: @@ -15868,209 +16213,6 @@ 1: 10 2 1 0 1: M END 1: -3: [03:09:33] Testing Github940: property dictionaries leaking memory -3: [03:09:33] done -3: Testing RDValue -3: Testing RDAny -3: dict set int vect -3: dict get int vect -3: static boost any:0.000219 s -3: dynamic boost any:0.001014 s -3: static RDAny:0.000125 s -3: dynamic RDAny:0.001059 s -3: static RDValue:1e-06 s -3: dynamic RDValue:0.000155 s -3: deleted! -3: [03:09:33] ------------------------------------- -3: [03:09:33] Testing String Pickle Roundtrips. -3: [03:09:33] done -3: [03:09:33] ------------------------------------- -3: [03:09:33] Testing conversion of vect to string. -3: [03:09:33] done -3: [03:09:33] ------------------------------------- -3: [03:09:33] Testing returning const references. -3: [03:09:33] any cast -3: [03:09:33] done: 0.000801 300000 -3: [03:09:33] copy -3: [03:09:33] done: 0.000834 300000 -3: [03:09:33] ref -3: [03:09:33] done: 0.0008 300000 -3: [03:09:33] dict -3: [03:09:33] done: 0.001954 300000 -3: [03:09:33] ref with hasVal -3: [03:09:33] done: 0.001301 300000 -3: [03:09:33] done -3: [03:09:33] ------------------------------------- -3: [03:09:33] Testing dict update. -3: [03:09:33] 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: [03:09:33] -5: ----------------------------------------- -5: [03:09:33] Finished: testPushAndPop() -5: [03:09:33] -5: ----------------------------------------- -5: [03:09:33] -5: ----------------------------------------- -6: Randomness seeded to: 868362758 -6: =============================================================================== -6: All tests passed (32 assertions in 2 test cases) -6: -7: [03:09:33] should not be silent -7: [03:09:33] should not be silent -7: Randomness seeded to: 3554970955 -7: [03:09:33] should not be silent -7: [03:09:33] should not be silent -7: [03:09:33] should not be silent -7: [03:09:33] should not be silent -7: [03:09:33] should not be silent -7: [03:09:33] should not be silent -7: [03:09:33] should not be silent -7: [03:09:33] should not be silent -7: =============================================================================== -7: All tests passed (26 assertions in 3 test cases) -7: -8: [03:09:33] pass -8: [03:09:33] v3 4 -8: [03:09:33] v4 5 -8: [03:09:33] SPARSE ----------------------------------- -8: [03:09:33] Set 10: 0 -8: [03:09:33] Set 11: 0 -8: [03:09:33] Set 14: 0 -8: [03:09:33] Set 10: 1 -8: [03:09:33] Get 14: 1 -8: [03:09:33] Num: 20 -8: [03:09:33] NumOn: 3 -8: [03:09:33] NumOff: 17 -8: 10, 11, 14, -8: [03:09:33] t2[19]: 0 -8: [03:09:33] t2[14]: 1 -8: [03:09:33] t2[19]: 0 -8: [03:09:33] 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: [03:09:33] Explicit ---------------------------------- -8: [03:09:33] Set 10: 0 -8: [03:09:33] Set 11: 0 -8: [03:09:33] Set 14: 0 -8: [03:09:33] Set 10: 1 -8: [03:09:33] Get 14: 1 -8: [03:09:33] Num: 20 -8: [03:09:33] NumOn: 3 -8: [03:09:33] NumOff: 17 -8: 10, 11, 14, -8: [03:09:33] t2[19]: 0 -8: [03:09:33] t2[14]: 1 -8: [03:09:33] t2[19]: 0 -8: [03:09:33] 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: [03:09:33] Done -8: [03:09:33] Test DiscreteValue Vectors 1 ---------------------------- -8: [03:09:33] Expected failure: Value out of range -8: [03:09:33] Expected failure: Value out of range -8: [03:09:33] Expected failure: Value out of range -8: [03:09:33] Expected failure: Value out of range -8: [03:09:33] Expected failure: Value out of range -8: [03:09:33] Test DiscreteValue Vectors 2 ------------------------------ -8: [03:09:33] Test DiscreteValue Vectors 3 --------------------------- -8: [03:09:33] Test DiscreteValue Operations ----------------------------- -8: [03:09:33] Test DiscreteValue Operations 2 -------------------------- -8: [03:09:33] Test SparseIntVect ------------------------------------ -8: [03:09:33] Test SparseIntVect Serialization -------------------------- -8: [03:09:33] Test BitVect Serialization ------------------------------- -8: [03:09:33] Test BitVect to FPS ------------------------------- -8: [03:09:33] Test BitVect to binary string ------------------------------- -8: [03:09:33] Test Similarity Measures BitVect ------------------------------- -8: [03:09:33] Test Similarity Measures SparseBitVect ------------------------------- -8: [03:09:33] Test BitVect with all ones ------------------------------- -8: [03:09:33] Test Explicit BitVects: Concatenation Operation ------------------------------- -8: [03:09:33] Test bitmap operations ------------------------------- -8: [03:09:33] Test bitmaps as properties ------------------------------- -8: [03:09:33] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- -8: [03:09:33] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- -8: [03:09:33] Test RealValue Vectors 2: L1Norm ------------------------------- -8: [03:09:33] Test RealValue Vectors 3: Pickles ------------------------------- -8: [03:09:33] Test RealValue Vectors 4: Vector Operations ------------------------------- -11: Randomness seeded to: 885262235 -11: =============================================================================== -11: All tests passed (3 assertions in 1 test case) -11: - 1/236 Test #3: testDict ............................... Passed 0.17 sec - 2/236 Test #4: testRDValue ............................ Passed 0.15 sec - 3/236 Test #6: dictTestsCatch ......................... Passed 0.11 sec - 4/236 Test #7: logTestsCatch .......................... Passed 0.10 sec - 5/236 Test #8: testDataStructs ........................ Passed 0.09 sec - 6/236 Test #9: testFPB ................................ Passed 0.06 sec - 7/236 Test #11: catchDataStructs ....................... Passed 0.03 sec -test 13 - Start 13: pyDiscreteValueVect - -13: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testDiscreteValueVect.py" -13: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap -13: Test timeout computed to be: 1500 -test 14 - Start 14: pyRealValueVect - -14: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testRealValueVect.py" -14: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap -14: Test timeout computed to be: 1500 -test 15 - Start 15: pySparseIntVect - -15: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testSparseIntVect.py" -15: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap -15: Test timeout computed to be: 1500 -test 16 - Start 16: pyFPB - -16: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataStructs/Wrap/testFPB.py" -16: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataStructs/Wrap -16: Test timeout computed to be: 1500 -test 17 - Start 17: testTransforms - -17: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/testTransforms -17: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry -17: Test timeout computed to be: 1500 -test 18 - Start 18: testGrid - -18: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/testGrid -18: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry -18: Test timeout computed to be: 1500 -test 19 - Start 19: testRealValueGrid - -19: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/testRealValueGrid -19: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry -19: Test timeout computed to be: 1500 1: github 4845 - nan coordinates but no crash 1: RDKit 2D 1: @@ -16163,125 +16305,7 @@ 1: 30 11 1 0 1: M END 1: -17: **************************************** -17: testPointND -17: **************************************** -17: testPointOps3D -17: **************************************** -17: testPointOps2D -17: **************************************** -17: test12D -17: ref1: 0.277285 0.52801 ref2: 1.37284 0.505525 -17: pt1: 1.41835 0.57852 pt2: 1.3061 1.27661 -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: - 8/236 Test #1: testCoordGen ........................... Passed 0.31 sec - 9/236 Test #10: testMultiFPB ........................... Passed 0.14 sec - 10/236 Test #17: testTransforms ......................... Passed 0.06 sec - 11/236 Test #18: testGrid ............................... Passed 0.04 sec -test 20 - Start 20: geometryTestsCatch - -20: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/geometryTestsCatch -20: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry -20: Test timeout computed to be: 1500 -test 21 - Start 21: testPyGeometry - -21: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/Geometry/Wrap/testGeometry.py" -21: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Geometry/Wrap -21: Test timeout computed to be: 1500 -test 22 - Start 22: testMatrices - -22: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/testMatrices -22: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics -22: Test timeout computed to be: 1500 -test 23 - Start 23: testConrec - -23: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/testConrec -23: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics -23: Test timeout computed to be: 1500 -19: *********************************************************** -19: Testing RealValueGrid3D -19: --------------------------------- -19: test1UniformRealValueGrid3D -19: -19: --------------------------------- -19: test2UniformRealValueGrid3DPickling -19: -19: --------------------------------- -19: test3UniformRealValueGrid3DIndexing -19: -19: --------------------------------- -19: test4UniformRealValueGrid3DOps -19: -20: Randomness seeded to: 1859732968 -20: =============================================================================== -20: All tests passed (50 assertions in 5 test cases) -20: -22: [03:09:34] ----------------------------------------- -22: [03:09:34] Testing RDNumerics: vectors and matrices Code -22: [03:09:34] --------------------------------------- -22: [03:09:34] test1Vector -22: [03:09:34] --------------------------------------- -22: [03:09:34] test2Matrix -22: [03:09:34] --------------------------------------- -22: [03:09:34] test3SquareMatrix -22: [03:09:34] --------------------------------------- -22: [03:09:34] 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-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment -24: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment -24: Test timeout computed to be: 1500 -test 25 - Start 25: pyAlignment - -25: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment/Wrap/testAlignment.py" -25: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap -25: Test timeout computed to be: 1500 -test 26 - Start 26: testOptimizer - -26: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer -26: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer -26: Test timeout computed to be: 1500 -23: Randomness seeded to: 1988415841 +23: Randomness seeded to: 3532216569 23: =============================================================================== 23: All tests passed (76 assertions in 3 test cases) 23: @@ -16296,21 +16320,28 @@ 24: --------------------------------------- 24: testReflection 24: --------------------------------------- -26: ------------------------------------- -26: Testing linear search. -26: done -26: ------------------------------------- -26: Testing BFGS optimization. -26: done - 15/236 Test #23: testConrec ............................. Passed 0.07 sec - 16/236 Test #24: testAlignment .......................... Passed 0.05 sec - 17/236 Test #26: testOptimizer .......................... Passed 0.02 sec + 14/236 Test #23: testConrec ............................. Passed 0.04 sec + 15/236 Test #24: testAlignment .......................... Passed 0.03 sec +test 26 + Start 26: testOptimizer + +26: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer +26: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/Numerics/Optimizer +26: Test timeout computed to be: 1500 test 27 Start 27: ForceFieldsCatch 27: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/ForceFieldsCatch 27: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField 27: Test timeout computed to be: 1500 +26: ------------------------------------- +26: Testing linear search. +26: done +26: ------------------------------------- +26: Testing BFGS optimization. +26: done + 16/236 Test #1: testCoordGen ........................... Passed 0.39 sec + 17/236 Test #26: testOptimizer .......................... Passed 0.03 sec test 28 Start 28: testUFFForceField @@ -16323,15 +16354,17 @@ 29: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField 29: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/MMFF 29: Test timeout computed to be: 1500 -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.033s -2: -2: OK -27: Randomness seeded to: 576305449 +27: Randomness seeded to: 35637591 27: =============================================================================== 27: All tests passed (20 assertions in 2 test cases) 27: + 18/236 Test #27: ForceFieldsCatch ....................... Passed 0.04 sec +test 30 + Start 30: pyForceFieldConstraints + +30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ForceField/Wrap/testConstraints.py" +30: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/Wrap +30: Test timeout computed to be: 1500 28: ------------------------------------- 28: Unit tests for force field basics. 28: done @@ -16378,48 +16411,28 @@ 28: done 28: ------------------------------------- 28: Unit tests for all UFF constraint terms. - 18/236 Test #27: ForceFieldsCatch ....................... Passed 0.05 sec -test 30 - Start 30: pyForceFieldConstraints - -30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ForceField/Wrap/testConstraints.py" -30: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ForceField/Wrap -30: Test timeout computed to be: 1500 +29: ------------------------------------- +29: Official MMFF validation suite. 13: ...... 13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.002s +13: Ran 6 tests in 0.006s 13: 13: OK -29: ------------------------------------- -29: Official MMFF validation suite. -14: ...... -14: ---------------------------------------------------------------------- -14: Ran 6 tests in 0.009s -14: -14: OK -28: done -28: ------------------------------------- -28: Unit tests for copying UFF ForceFields. -15: ......... -15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.013s -15: -15: OK -28: done -28: ------------------------------------- -28: Unit test for UFF butane scan. -16: ......... -16: ---------------------------------------------------------------------- -16: Ran 9 tests in 0.072s -16: -16: OK - 19/236 Test #2: pyCoordGen ............................. Passed 0.56 sec +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.061s +2: +2: OK + 19/236 Test #13: pyDiscreteValueVect .................... Passed 0.38 sec test 31 Start 31: testDistGeom 31: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom/testDistGeom 31: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom 31: Test timeout computed to be: 1500 +28: done +28: ------------------------------------- +28: Unit tests for copying UFF ForceFields. 31: *********************************************************** 31: test1 31: *********************************************************** @@ -16431,244 +16444,182 @@ 31: 1 1 1 0 31: *********************************************************** 31: - 20/236 Test #31: testDistGeom ........................... Passed 0.05 sec + 20/236 Test #31: testDistGeom ........................... Passed 0.04 sec test 32 Start 32: pyDistGeom 32: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DistGeom/Wrap/rough_test.py" 32: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DistGeom/Wrap 32: Test timeout computed to be: 1500 - 21/236 Test #13: pyDiscreteValueVect .................... Passed 0.45 sec - 22/236 Test #14: pyRealValueVect ........................ Passed 0.44 sec +28: done +28: ------------------------------------- +28: Unit test for UFF butane scan. +14: ...... +14: ---------------------------------------------------------------------- +14: Ran 6 tests in 0.001s +14: +14: OK +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... +15: ......... +15: ---------------------------------------------------------------------- +15: Ran 9 tests in 0.012s +15: +15: OK +16: ......... +16: ---------------------------------------------------------------------- +16: Ran 9 tests in 0.071s +16: +16: OK + 21/236 Test #2: pyCoordGen ............................. Passed 0.65 sec test 33 Start 33: graphmolcpTest 33: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolcpTest 33: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 33: Test timeout computed to be: 1500 +33: +33: +33: +33: COPY + 22/236 Test #33: graphmolcpTest ......................... Passed 0.03 sec test 34 Start 34: graphmolqueryTest 34: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest 34: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 34: Test timeout computed to be: 1500 -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... -33: -33: -33: -33: COPY - 23/236 Test #15: pySparseIntVect ........................ Passed 0.51 sec - 24/236 Test #16: pyFPB .................................. Passed 0.49 sec - 25/236 Test #33: graphmolcpTest ......................... Passed 0.08 sec +34: [23:38:03] ---------------------- Test1 +34: [23:38:03] Done! +34: [23:38:03] ---------------------- Test2 +34: [23:38:03] Done! +34: [23:38:03] ---------------------- Test3 +34: [23:38:03] Done! +34: [23:38:03] ---------------------- Test4 +34: [23:38:03] Done! +34: [23:38:03] ---------------------- Test5 +34: [23:38:03] Done! +34: [23:38:03] +34: +34: **** +34: Pre-condition Violation +34: Can't expand empty query +34: Violation occurred on line 30 in file ./Code/GraphMol/QueryAtom.cpp +34: Failed Expression: dp_query +34: ---------- +34: Stacktrace: +34: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +34: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +34: 2# RDKit::QueryAtom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +34: 3# 0x0000AAAACB813610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 4# 0x0000AAAACB810A88 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 5# 0x0000FFFF8952229C in /lib/aarch64-linux-gnu/libc.so.6 +34: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +34: 7# 0x0000AAAACB810B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: ---------- +34: **** +34: +34: [23:38:03] Done! +34: [23:38:03] ---------------------- Test issue 2892580 +34: [23:38:03] Done! +34: [23:38:03] ---------------------- Test github issue 53: query molecules not matching [R] +34: [23:38:03] Done! +34: [23:38:03] ---------------------- Test queries using qualifiers instead of == +34: [23:38:03] Done! +34: [23:38:03] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +34: [23:38:03] Done! +34: [23:38:03] ---------------------- Test extra atom queries +34: [23:38:03] Done! +34: [23:38:03] ---------------------- Test extra bond queries +34: [23:38:03] Done! +34: [23:38:03] ---------------------- Test num heteroatom neighbor queries +34: [23:38:03] Done! +34: [23:38:03] ---------------------- Test atom type queries +34: [23:38:03] Done! +34: [23:38:03] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +34: [23:38:03] Done! +34: [23:38:03] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +34: [23:38:03] Done! + 23/236 Test #34: graphmolqueryTest ...................... Passed 0.03 sec test 35 Start 35: graphmolMolOpsTest 35: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMolOpsTest 35: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 35: Test timeout computed to be: 1500 + 24/236 Test #15: pySparseIntVect ........................ Passed 0.56 sec test 36 Start 36: graphmoltestChirality 36: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestChirality 36: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 36: Test timeout computed to be: 1500 + 25/236 Test #14: pyRealValueVect ........................ Passed 0.59 sec test 37 Start 37: graphmoltestPickler 37: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPickler 37: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 37: Test timeout computed to be: 1500 -34: [03:09:34] ---------------------- Test1 -34: [03:09:34] Done! -34: [03:09:34] ---------------------- Test2 -34: [03:09:34] Done! -34: [03:09:34] ---------------------- Test3 -34: [03:09:34] Done! -34: [03:09:34] ---------------------- Test4 -34: [03:09:34] Done! -34: [03:09:34] ---------------------- Test5 -34: [03:09:34] Done! -34: [03:09:34] -34: -34: **** -34: Pre-condition Violation -34: Can't expand empty query -34: Violation occurred on line 30 in file ./Code/GraphMol/QueryAtom.cpp -34: Failed Expression: dp_query -34: ---------- -34: Stacktrace: -34: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -34: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -34: 2# RDKit::QueryAtom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -34: 3# 0x0000AAAAB4443610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 4# 0x0000AAAAB4440A88 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 5# 0x0000FFFFAAF6229C in /lib/aarch64-linux-gnu/libc.so.6 -34: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -34: 7# 0x0000AAAAB4440B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: ---------- -34: **** -34: -34: [03:09:34] Done! -34: [03:09:34] ---------------------- Test issue 2892580 -34: [03:09:34] Done! -34: [03:09:34] ---------------------- Test github issue 53: query molecules not matching [R] -34: [03:09:34] Done! -34: [03:09:34] ---------------------- Test queries using qualifiers instead of == -34: [03:09:34] Done! -34: [03:09:34] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -34: [03:09:34] Done! -34: [03:09:34] ---------------------- Test extra atom queries -34: [03:09:34] Done! -34: [03:09:34] ---------------------- Test extra bond queries -34: [03:09:34] Done! -34: [03:09:34] ---------------------- Test num heteroatom neighbor queries -34: [03:09:34] Done! -34: [03:09:34] ---------------------- Test atom type queries -34: [03:09:34] Done! -34: [03:09:34] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -34: [03:09:34] Done! -34: [03:09:34] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -34: [03:09:34] Done! 21: .................... 21: ---------------------------------------------------------------------- -21: Ran 20 tests in 0.045s +21: Ran 20 tests in 0.077s 21: 21: OK 21: Testing Geometry wrapper +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing String Pickle Roundtrips. 35: 1 1 2 35: 1 1 1 35: 2 1 0.75 -35: path: 2 - 26/236 Test #34: graphmolqueryTest ...................... Passed 0.11 sec + 26/236 Test #16: pyFPB .................................. Passed 0.58 sec test 38 Start 38: graphmoltestPicklerGlobalSetting 38: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting 38: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 38: Test timeout computed to be: 1500 -35: [03:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: [03:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: [03:09:34] Explicit valence for atom # 0 B, 5, is greater than permitted -35: [03:09:34] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [03:09:34] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [03:09:34] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [03:09:34] Explicit valence for atom # 1 Si, 7, is greater than permitted -36: -------------------------- -36: -------------------------- -36: C/C=C/C(C)Cl -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing String Pickle Roundtrips. -36: [03:09:34] Conflicting single bond directions around double bond at index 2. -36: [03:09:34] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [03:09:34] Conflicting single bond directions around double bond at index 4. -36: [03:09:34] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [03:09:34] Conflicting single bond directions around double bond at index 15. -36: [03:09:34] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [03:09:34] Conflicting single bond directions around double bond at index 2. -36: [03:09:34] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [03:09:34] Conflicting single bond directions around double bond at index 1. -36: [03:09:34] BondStereo set to STEREONONE and single bond directions set to NONE. -28: done - 27/236 Test #28: testUFFForceField ...................... Passed 0.36 sec +35: path: 2 +35: [23:38:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +35: [23:38:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +35: [23:38:03] Explicit valence for atom # 0 B, 5, is greater than permitted +35: [23:38:03] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [23:38:03] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [23:38:03] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [23:38:03] Explicit valence for atom # 1 Si, 7, is greater than permitted +38: [23:38:03] done + 27/236 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.03 sec test 39 Start 39: graphmolIterTest 39: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolIterTest 39: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 39: Test timeout computed to be: 1500 +36: -------------------------- +36: -------------------------- +36: C/C=C/C(C)Cl 25: ..... 25: ---------------------------------------------------------------------- -25: Ran 5 tests in 0.009s +25: Ran 5 tests in 0.001s 25: 25: OK 25: Testing Alignment Wrapper code: -36: -------------------------------------------------- -38: [03:09:34] done - 28/236 Test #21: testPyGeometry ......................... Passed 0.51 sec - 29/236 Test #36: graphmoltestChirality .................. Passed 0.10 sec - 30/236 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.07 sec -test 40 - Start 40: hanoiTest - -40: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/hanoiTest -40: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -40: Test timeout computed to be: 1500 -test 41 - Start 41: graphmolMemTest1 - -41: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMemTest1 -41: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -41: Test timeout computed to be: 1500 -test 42 - Start 42: resMolSupplierTest - -42: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/resMolSupplierTest -42: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -42: Test timeout computed to be: 1500 -35: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 -35: [03:09:34] non-ring atom 0 marked aromatic -35: [03:09:34] non-ring atom 0 marked aromatic -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing reading existing pickle file (v2). -40: [03:09:34] Testing the hanoi sort -40: [03:09:34] populating vectors - 31/236 Test #39: graphmolIterTest ....................... Passed 0.08 sec - 32/236 Test #41: graphmolMemTest1 ....................... Passed 0.02 sec -test 43 - Start 43: molBundleTest - -43: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/molBundleTest -43: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -43: Test timeout computed to be: 1500 -test 44 - Start 44: testSGroup - -44: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/testSGroup -44: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -44: Test timeout computed to be: 1500 -35: [03:09:34] Conflicting single bond directions around double bond at index 17. -35: [03:09:34] BondStereo set to STEREONONE and single bond directions set to NONE. -35: starting ring finding -35: done -35: starting ring finding -35: done -35: starting ring finding -35: done -35: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C -35: starting sanitization -35: done -35: starting sanitization -35: done -35: starting ring finding -35: done - 33/236 Test #43: molBundleTest .......................... Passed 0.04 sec -test 45 - Start 45: test-valgrind - -45: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind -45: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -45: Test timeout computed to be: 1500 -35: starting ring finding -35: done -35: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 -35: [03:09:34] WARNING: not removing hydrogen atom with dummy atom neighbors -35: ------------------------------- -35: [03:09:34] Explicit valence for atom # 0 N, 4, is greater than permitted -35: [03:09:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [03:09:34] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -35: [03:09:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [03:09:34] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [03:09:34] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [03:09:34] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [03:09:34] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [03:09:34] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: -35: [03:09:34] WARNING: not removing hydrogen atom with dummy atom neighbors -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing combining molecules using pickles. +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing reading existing pickle file (v2). +36: [23:38:03] Conflicting single bond directions around double bond at index 2. +36: [23:38:03] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [23:38:03] Conflicting single bond directions around double bond at index 4. +36: [23:38:03] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [23:38:03] Conflicting single bond directions around double bond at index 15. +36: [23:38:03] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [23:38:03] Conflicting single bond directions around double bond at index 2. +36: [23:38:03] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [23:38:03] Conflicting single bond directions around double bond at index 1. +36: [23:38:03] BondStereo set to STEREONONE and single bond directions set to NONE. +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing combining molecules using pickles. 37: Atoms: 37: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 37: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 @@ -16685,37 +16636,44 @@ 37: 4 4->5 order: 1 37: 5 5->6 order: 1 37: 6 6->3 order: 1 -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing Issue164: Roundtrip Pickle Failure. -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing Issue219: Pickle Failure with Conformations. -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing Issue220: Pickle problems with bond stereochemistry. -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing query serialization. -37: [03:09:34] C=[$(C=O)] -37: [03:09:34] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing radical handling in pickles. -37: [03:09:34] done -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing sf.net issue 2788233. -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing sf.net issue 3202580. +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing Issue164: Roundtrip Pickle Failure. +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing Issue219: Pickle Failure with Conformations. +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing Issue220: Pickle problems with bond stereochemistry. +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing query serialization. +37: [23:38:03] C=[$(C=O)] +37: [23:38:03] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing radical handling in pickles. +37: [23:38:03] done + 28/236 Test #39: graphmolIterTest ....................... Passed 0.04 sec +test 40 + Start 40: hanoiTest + +40: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/hanoiTest +40: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +40: Test timeout computed to be: 1500 +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing sf.net issue 2788233. +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing sf.net issue 3202580. 37: mass! 13.0034 -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing sf.net issue 3316407. -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing sf.net issue 3496759. +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing sf.net issue 3316407. +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing sf.net issue 3496759. 37: smi match: *C *C 37: smi match: **=* **=* 37: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O @@ -16809,26 +16767,12 @@ 37: smi match: O=C1CCO1 O=C1CCO1 37: smi match: C=C(S)[SH]=O C=C(S)[SH]=O 37: smi match: C=CCO C=CCO - 34/236 Test #25: pyAlignment ............................ Passed 0.60 sec - 35/236 Test #44: testSGroup ............................. Passed 0.09 sec 37: smi match: C=CC=N C=CC=N 37: smi match: C=CC=O C=CC=O 37: smi match: C=CC(=O)C=C C=CC(=O)C=C 37: smi match: C=CC=S C=CC=S 37: smi match: C=CC(=S)S C=CC(=S)S 37: smi match: *C=C(*)C=C *C=C(*)C=C -test 46 - Start 46: graphmolTestsCatch - -46: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -46: Test timeout computed to be: 1500 -test 47 - Start 47: graphmolOrganometallicsCatch - -47: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch -47: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -47: Test timeout computed to be: 1500 37: smi match: C=CC=N C=CC=N 37: smi match: *N(*)C=C *N(*)C=C 37: smi match: C=CN(=O)=O C=CN(=O)=O @@ -16894,6 +16838,13 @@ 37: smi match: c=S c=S 37: smi match: S=CS S=CS 37: smi match: C=CN(=O)=O C=CN(=O)=O +32: ...... +32: ---------------------------------------------------------------------- +32: Ran 6 tests in 0.001s +32: +32: OK +36: -------------------------------------------------- +35: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 37: smi match: C=CN(=O)O C=CN(=O)O 37: smi match: N=CC=O N=CC=O 37: smi match: C=CS C=CS @@ -16987,52 +16938,347 @@ 37: smi match: CS(=O)(=O)[O-] CS(=O)(=O)[O-] 37: smi match: NS(=O)(=O)[O-] NS(=O)(=O)[O-] 37: smi match: *C(*)(*)C=O *C(*)(*)C=O -32: ...... -32: ---------------------------------------------------------------------- -32: Ran 6 tests in 0.001s -32: -32: OK -46: Randomness seeded to: 2500146860 -46: [03:09:34] WARNING: not removing hydrogen atom without neighbors -46: [03:09:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:09:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:09:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:09:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:09:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:09:34] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [03:09:34] Explicit valence for atom # 1 N, 6, is greater than permitted -46: [03:09:34] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [03:09:34] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [03:09:34] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [03:09:34] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [03:09:34] non-ring atom 2 marked aromatic -46: [03:09:34] non-ring atom 2 marked aromatic -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [03:09:34] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [03:09:34] Explicit valence for atom # 4 F, 2, is greater than permitted -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 6 7 8 -46: [03:09:34] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [03:09:34] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [03:09:34] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [03:09:34] WARNING: not removing hydrogen atom with wedged bond -46: [03:09:34] WARNING: not removing hydrogen atom without neighbors -46: [03:09:34] WARNING: not removing hydrogen atom without neighbors -46: [03:09:34] WARNING: not removing hydrogen atom without neighbors -46: [03:09:34] WARNING: not removing hydrogen atom without neighbors -46: [03:09:34] Unreasonable formal charge on atom # 0. - 36/236 Test #45: test-valgrind .......................... Passed 0.14 sec +37: smi match: *C(*)(*)C=O *C(*)(*)C=O +37: smi match: *C(*)C=O *C(*)C=O +37: smi match: *CC=O *CC=O +37: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O +37: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O +37: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O +37: smi match: *C[SH](=O)=O *C[SH](=O)=O + 29/236 Test #36: graphmoltestChirality .................. Passed 0.14 sec +test 41 + Start 41: graphmolMemTest1 + +41: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMemTest1 +41: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +41: Test timeout computed to be: 1500 +40: [23:38:03] Testing the hanoi sort +40: [23:38:03] populating vectors +37: smi match: * * +37: smi match: *1CC1 *1CC1 +37: smi match: O=COC=O O=COC=O +37: smi match: N=C=O N=C=O +37: smi match: N=C=S N=C=S +37: smi match: O~O O~O +37: smi match: N~[SiH4] N~[SiH4] +37: smi match: *P *P +37: smi match: C=N=N C=N=N +37: smi match: *N#[NH+] *N#[NH+] +37: smi match: *S* *S* +37: smi match: ** ** +37: smi match: *CC* *CC* +37: smi match: *O[SiH3] *O[SiH3] +37: smi match: *OS(*)~O *OS(*)~O +37: smi match: N~N~O N~N~O +37: smi match: *N(~O)(~O)~O *N(~O)(~O)~O +37: smi match: *[N+](=C)[O-] *[N+](=C)[O-] +37: smi match: * * +37: smi match: *C(*)NCN(*)* *C(*)NCN(*)* +37: smi match: *OCC#N *OCC#N +37: smi match: **C=C **C=C +37: smi match: C=C[O-] C=C[O-] +37: smi match: C=CO C=CO +37: smi match: * * +37: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O +37: smi match: O=COn1ccnc1 O=COn1ccnc1 +37: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F +37: smi match: CC(C)(C)S CC(C)(C)S +37: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C +37: smi match: [CH]=O [CH]=O +37: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C +37: smi match: SS SS +37: smi match: [SH] [SH] +37: smi match: *C* *C* +37: smi match: * * +37: smi match: C[nH3+] C[nH3+] +37: smi match: cC(=N)[NH2] cC(=N)[NH2] +37: smi match: O=CN[OH] O=CN[OH] +37: smi match: NN NN +37: smi match: * * +37: smi match: *OP(=O)O* *OP(=O)O* +37: smi match: * * +37: smi match: * * +37: smi match: * * +37: smi match: *N=C(*)* *N=C(*)* +37: smi match: *C(*)(*)C=O *C(*)(*)C=O +37: smi match: CSC=O CSC=O +37: smi match: * * +37: smi match: O=CCl O=CCl +37: smi match: *** *** +37: smi match: *C=O *C=O +37: smi match: C[OH] C[OH] +37: smi match: C[OH] C[OH] +37: smi match: C[OH] C[OH] +37: smi match: C[OH] C[OH] +37: smi match: C[CH]=O C[CH]=O +37: smi match: *=* *=* +37: smi match: *C *C +37: smi match: C#C C#C +37: smi match: *[CH]C=C *[CH]C=C +37: smi match: cCC(=O)[OH] cCC(=O)[OH] +37: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] +37: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] +37: smi match: C=CC(=O)[OH] C=CC(=O)[OH] +37: smi match: N#CC(=O)[OH] N#CC(=O)[OH] +37: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O +37: smi match: *N(*)C*=O *N(*)C*=O +37: smi match: O=*C[OH] O=*C[OH] +37: smi match: *=C*=O *=C*=O +37: smi match: *=CC#N *=CC#N +37: smi match: *C[OH] *C[OH] +37: smi match: ** ** +37: smi match: *C[OH] *C[OH] +37: smi match: *C(*)=O *C(*)=O +37: smi match: * * +37: smi match: *CC(=O)[OH] *CC(=O)[OH] +37: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O +37: smi match: *c *c +37: smi match: CN(C)c CN(C)c +37: smi match: c c +37: smi match: *c *c +37: smi match: *c *c +37: smi match: **:*cF **:*cF +37: smi match: cB([OH])[OH] cB([OH])[OH] +37: smi match: N~N~N N~N~N +37: smi match: *N=N* *N=N* +37: smi match: *CC[OH] *CC[OH] +37: smi match: *CC[OH] *CC[OH] +37: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] +37: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] +37: smi match: *CCC(=O)[OH] *CCC(=O)[OH] +37: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] +37: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O +35: [23:38:03] non-ring atom 0 marked aromatic +35: [23:38:03] non-ring atom 0 marked aromatic +37: smi match: *OC(*)=O *OC(*)=O +37: smi match: *C(=O)[OH] *C(=O)[OH] +37: smi match: O=C[OH] O=C[OH] +37: smi match: *OC(=O)O* *OC(=O)O* +37: smi match: * * +37: smi match: *OC(=O)Cl *OC(=O)Cl +37: smi match: *C#N *C#N +37: smi match: NCC(=O)NCC=O NCC(=O)NCC=O +37: smi match: SS SS +37: smi match: * * +37: smi match: *=* *=* +37: smi match: *=* *=* +37: smi match: *=* *=* +37: smi match: *=* *=* +37: smi match: C1CO1 C1CO1 +37: smi match: *OC(*)=O *OC(*)=O +37: smi match: * * +37: smi match: *O*[OH] *O*[OH] +37: smi match: COC(C)(C)O COC(C)(C)O +37: smi match: *[OH] *[OH] +37: smi match: ** ** +37: smi match: C=N[NH2] C=N[NH2] +37: smi match: C=NC=O C=NC=O +37: smi match: * * +37: smi match: C#NC C#NC +37: smi match: CN=C=O CN=C=O +37: smi match: CN=C=S CN=C=S +37: smi match: *OC(*)(*)O* *OC(*)(*)O* +37: smi match: *C(*)=O *C(*)=O +37: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C +37: smi match: *~*=O *~*=O +37: smi match: *~*=O *~*=O +37: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] +37: smi match: * * +37: smi match: *C#N *C#N +37: smi match: *N(=O)~O *N(=O)~O +37: smi match: N N +37: smi match: OC(=O)C(O)=O OC(=O)C(O)=O +37: smi match: C=NO C=NO +37: smi match: O~O O~O +37: smi match: c[OH] c[OH] +37: smi match: O=P(~[OH])~O O=P(~[OH])~O +37: smi match: CO~P(=O)~O CO~P(=O)~O +37: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O +37: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O +37: smi match: O=P(~O)~O O=P(~O)~O +37: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O +37: smi match: C[NH2] C[NH2] +37: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 +37: smi match: * * +37: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 +37: smi match: CS(C)~O CS(C)~O +37: smi match: CS(C)(~O)~O CS(C)(~O)~O +37: smi match: CS(N)(~O)~O CS(N)(~O)~O +37: smi match: CS([OH])(~O)~O CS([OH])(~O)~O +37: smi match: COS(C)(~O)~O COS(C)(~O)~O +37: smi match: *S(C)(~O)~O *S(C)(~O)~O +37: smi match: CN(C)C CN(C)C +37: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 +37: smi match: *C(*)=S *C(*)=S +37: smi match: *OC(*)=S *OC(*)=S +37: smi match: * * +37: smi match: C[SH] C[SH] +37: smi match: c[SH] c[SH] +37: smi match: NC(N)=S NC(N)=S +37: smi match: * * +37: smi match: ***** ***** +37: smi match: NC(N)=O NC(N)=O +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing sf.net issue 280. +35: [23:38:03] Conflicting single bond directions around double bond at index 17. +35: [23:38:03] BondStereo set to STEREONONE and single bond directions set to NONE. +35: starting ring finding +35: done +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing sf.net issue 285. +37: [23:38:03] done +37: [23:38:03] done +37: [23:38:03] done +37: [23:38:03] done +37: [23:38:03] done +37: [23:38:03] done +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing Github2441: Add RDProps interface to Conformers. +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing Issue2510: Pickle Confs as double. +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing loading pickled mols with conformers +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing conformer reading/writing options +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing property reading options +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing property reading options +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing boost::serialization integration +37: [23:38:03] done +37: [23:38:03] ------------------------------------- +37: [23:38:03] Testing github issue 6036 + 30/236 Test #37: graphmoltestPickler .................... Passed 0.15 sec + 31/236 Test #41: graphmolMemTest1 ....................... Passed 0.03 sec +test 42 + Start 42: resMolSupplierTest + +42: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/resMolSupplierTest +42: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +42: Test timeout computed to be: 1500 +test 43 + Start 43: molBundleTest + +43: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/molBundleTest +43: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +43: Test timeout computed to be: 1500 +35: starting ring finding +35: done +35: starting ring finding +35: done +35: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C +35: starting sanitization +35: done +35: starting sanitization +28: done + 32/236 Test #21: testPyGeometry ......................... Passed 0.66 sec + 33/236 Test #25: pyAlignment ............................ Passed 0.58 sec + 34/236 Test #28: testUFFForceField ...................... Passed 0.54 sec +test 44 + Start 44: testSGroup + +44: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/testSGroup +44: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +44: Test timeout computed to be: 1500 +test 45 + Start 45: test-valgrind + +45: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind +45: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +45: Test timeout computed to be: 1500 +test 46 + Start 46: graphmolTestsCatch + +46: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +46: Test timeout computed to be: 1500 +35: done +35: starting ring finding +35: done +35: starting ring finding +35: done +35: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 +35: [23:38:03] WARNING: not removing hydrogen atom with dummy atom neighbors +35: ------------------------------- +35: [23:38:03] Explicit valence for atom # 0 N, 4, is greater than permitted + 35/236 Test #32: pyDistGeom ............................. Passed 0.40 sec + 36/236 Test #43: molBundleTest .......................... Passed 0.06 sec +test 47 + Start 47: graphmolOrganometallicsCatch + +47: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch +47: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +47: Test timeout computed to be: 1500 test 48 Start 48: graphmolSGroupCatch 48: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolSGroupCatch 48: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 48: Test timeout computed to be: 1500 -46: [03:09:34] +35: [23:38:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +35: [23:38:03] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +35: [23:38:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +35: [23:38:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [23:38:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [23:38:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [23:38:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [23:38:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: +46: Randomness seeded to: 3949451462 +46: [23:38:03] WARNING: not removing hydrogen atom without neighbors +46: [23:38:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [23:38:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [23:38:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [23:38:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [23:38:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. + 37/236 Test #45: test-valgrind .......................... Passed 0.05 sec +test 49 + Start 49: graphmolAdjustQueryCatch + +49: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch +49: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +49: Test timeout computed to be: 1500 +46: [23:38:03] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [23:38:03] Explicit valence for atom # 1 N, 6, is greater than permitted +46: [23:38:03] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [23:38:03] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [23:38:03] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [23:38:03] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [23:38:03] non-ring atom 2 marked aromatic +46: [23:38:03] non-ring atom 2 marked aromatic +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [23:38:03] Explicit valence for atom # 1 O, 3, is greater than permitted +46: [23:38:03] Explicit valence for atom # 4 F, 2, is greater than permitted +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 6 7 8 +46: [23:38:03] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [23:38:03] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [23:38:03] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [23:38:03] WARNING: not removing hydrogen atom with wedged bond +46: [23:38:03] WARNING: not removing hydrogen atom without neighbors +46: [23:38:03] WARNING: not removing hydrogen atom without neighbors +46: [23:38:03] WARNING: not removing hydrogen atom without neighbors +46: [23:38:03] WARNING: not removing hydrogen atom without neighbors +46: [23:38:03] Unreasonable formal charge on atom # 0. +35: [23:38:03] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17044,20 +17290,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE353C1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC64C1A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17069,20 +17315,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE353C218 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC64C218 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17094,20 +17340,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE353C298 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC64C298 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17119,20 +17365,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE353C360 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC64C360 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17144,20 +17390,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE353C3D8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC64C3D8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17169,20 +17415,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE353C45C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC64C45C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17194,20 +17440,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE353CB70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC64CB70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17219,20 +17465,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE353C58C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC64C58C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17244,20 +17490,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE353C610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC64C610 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17269,20 +17515,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE353CB54 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC64CB54 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17294,20 +17540,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE353C800 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC64C800 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17319,24 +17565,24 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE353CB34 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC64CB34 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:09:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:09:34] WARNING: not removing hydrogen atom without neighbors -46: [03:09:34] Explicit valence for atom # 1 F greater than permitted -46: [03:09:34] +46: [23:38:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [23:38:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [23:38:03] WARNING: not removing hydrogen atom without neighbors +46: [23:38:03] Explicit valence for atom # 1 F greater than permitted +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17348,22 +17594,29 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE34EAB6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC5FAB6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] +46: [23:38:03] 46: 46: **** + 38/236 Test #44: testSGroup ............................. Passed 0.10 sec +test 50 + Start 50: chiralityTestsCatch + +50: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/chiralityTestsCatch +50: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol +50: Test timeout computed to be: 1500 46: Pre-condition Violation 46: plain atoms have no Query 46: Violation occurred on line 702 in file ./Code/GraphMol/Atom.cpp @@ -17373,20 +17626,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE34EABF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC5FABF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17398,20 +17651,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE34EA7BC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC5FA7BC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] +46: [23:38:03] 46: 46: **** 46: Pre-condition Violation @@ -17423,312 +17676,71 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x0000AAAAE34EA848 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x0000AAAAE35883CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x0000AAAAE3588D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x0000AAAAE35891B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x0000AAAAE355C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x0000AAAAE355CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x0000AAAAE34DE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x0000FFFF8846229C in /lib/aarch64-linux-gnu/libc.so.6 +46: 3# 0x0000AAAAAC5FA848 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000AAAAAC6983CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000AAAAAC698D80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000AAAAAC6991B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000AAAAAC66C598 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000AAAAAC66CAE4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000AAAAAC5EE090 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x0000FFFF9907229C in /lib/aarch64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -46: 12# 0x0000AAAAE34DE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000AAAAAC5EE170 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -37: smi match: *C(*)(*)C=O *C(*)(*)C=O -37: smi match: *C(*)C=O *C(*)C=O -37: smi match: *CC=O *CC=O -37: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O -37: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O -37: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O -37: smi match: *C[SH](=O)=O *C[SH](=O)=O -37: smi match: * * -37: smi match: *1CC1 *1CC1 -37: smi match: O=COC=O O=COC=O -37: smi match: N=C=O N=C=O -37: smi match: N=C=S N=C=S -37: smi match: O~O O~O -37: smi match: N~[SiH4] N~[SiH4] -37: smi match: *P *P -37: smi match: C=N=N C=N=N -37: smi match: *N#[NH+] *N#[NH+] -37: smi match: *S* *S* -37: smi match: ** ** -37: smi match: *CC* *CC* -37: smi match: *O[SiH3] *O[SiH3] -37: smi match: *OS(*)~O *OS(*)~O -37: smi match: N~N~O N~N~O -37: smi match: *N(~O)(~O)~O *N(~O)(~O)~O -37: smi match: *[N+](=C)[O-] *[N+](=C)[O-] -37: smi match: * * -37: smi match: *C(*)NCN(*)* *C(*)NCN(*)* -37: smi match: *OCC#N *OCC#N -37: smi match: **C=C **C=C -46: [03:09:34] Unusual charge on atom 0 number of radical electrons set to zero -46: [03:09:34] Unusual charge on atom 0 number of radical electrons set to zero -46: [03:09:34] Unusual charge on atom 0 number of radical electrons set to zero -46: [03:09:34] non-ring atom 0 marked aromatic -46: [03:09:34] non-ring atom 0 marked aromatic -46: [03:09:34] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [03:09:34] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [03:09:34] Explicit valence for atom # 3 N, 4, is greater than permitted -46: [03:09:34] Explicit valence for atom # 15 C, 5, is greater than permitted -46: [03:09:34] Explicit valence for atom # 11 C, 5, is greater than permitted -46: [03:09:34] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [03:09:34] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [03:09:34] Explicit valence for atom # 9 C, 6, is greater than permitted -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 7 -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 3 -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 3 7 -46: [03:09:34] Can't kekulize mol. Unkekulized atoms: 3 7 -37: smi match: C=C[O-] C=C[O-] -37: smi match: C=CO C=CO -37: smi match: * * -37: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O -37: smi match: O=COn1ccnc1 O=COn1ccnc1 -37: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F -37: smi match: CC(C)(C)S CC(C)(C)S -37: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C -37: smi match: [CH]=O [CH]=O -37: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C -37: smi match: SS SS -37: smi match: [SH] [SH] -37: smi match: *C* *C* -37: smi match: * * -37: smi match: C[nH3+] C[nH3+] -37: smi match: cC(=N)[NH2] cC(=N)[NH2] -37: smi match: O=CN[OH] O=CN[OH] -37: smi match: NN NN -37: smi match: * * -37: smi match: *OP(=O)O* *OP(=O)O* -37: smi match: * * -37: smi match: * * -46: [03:09:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -30: ...[03:09:34] Molecule does not have explicit Hs. Consider calling AddHs() -46: [03:09:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -37: smi match: * * -37: smi match: *N=C(*)* *N=C(*)* -37: smi match: *C(*)(*)C=O *C(*)(*)C=O -37: smi match: CSC=O CSC=O -37: smi match: * * -37: smi match: O=CCl O=CCl -37: smi match: *** *** -37: smi match: *C=O *C=O -37: smi match: C[OH] C[OH] -37: smi match: C[OH] C[OH] -37: smi match: C[OH] C[OH] -37: smi match: C[OH] C[OH] -37: smi match: C[CH]=O C[CH]=O -37: smi match: *=* *=* -37: smi match: *C *C -37: smi match: C#C C#C -37: smi match: *[CH]C=C *[CH]C=C -37: smi match: cCC(=O)[OH] cCC(=O)[OH] -37: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] -37: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] -37: smi match: C=CC(=O)[OH] C=CC(=O)[OH] -37: smi match: N#CC(=O)[OH] N#CC(=O)[OH] -37: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O -37: smi match: *N(*)C*=O *N(*)C*=O -37: smi match: O=*C[OH] O=*C[OH] -37: smi match: *=C*=O *=C*=O -37: smi match: *=CC#N *=CC#N -37: smi match: *C[OH] *C[OH] -37: smi match: ** ** -37: smi match: *C[OH] *C[OH] -37: smi match: *C(*)=O *C(*)=O -37: smi match: * * -37: smi match: *CC(=O)[OH] *CC(=O)[OH] -37: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O -37: smi match: *c *c -37: smi match: CN(C)c CN(C)c -37: smi match: c c -37: smi match: *c *c -37: smi match: *c *c -37: smi match: **:*cF **:*cF -37: smi match: cB([OH])[OH] cB([OH])[OH] -37: smi match: N~N~N N~N~N -37: smi match: *N=N* *N=N* -37: smi match: *CC[OH] *CC[OH] -37: smi match: *CC[OH] *CC[OH] -37: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] -37: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] -37: smi match: *CCC(=O)[OH] *CCC(=O)[OH] -37: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] -37: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O -37: smi match: *OC(*)=O *OC(*)=O -37: smi match: *C(=O)[OH] *C(=O)[OH] -37: smi match: O=C[OH] O=C[OH] -37: smi match: *OC(=O)O* *OC(=O)O* -37: smi match: * * -37: smi match: *OC(=O)Cl *OC(=O)Cl -37: smi match: *C#N *C#N -37: smi match: NCC(=O)NCC=O NCC(=O)NCC=O -37: smi match: SS SS -37: smi match: * * -37: smi match: *=* *=* -37: smi match: *=* *=* -37: smi match: *=* *=* -37: smi match: *=* *=* -37: smi match: C1CO1 C1CO1 -37: smi match: *OC(*)=O *OC(*)=O -48: Randomness seeded to: 1838672125 -48: =============================================================================== -48: All tests passed (136 assertions in 8 test cases) -48: - 37/236 Test #48: graphmolSGroupCatch .................... Passed 0.06 sec -test 49 - Start 49: graphmolAdjustQueryCatch - -49: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch -49: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -49: Test timeout computed to be: 1500 -37: smi match: * * -37: smi match: *O*[OH] *O*[OH] -37: smi match: COC(C)(C)O COC(C)(C)O -37: smi match: *[OH] *[OH] -37: smi match: ** ** -37: smi match: C=N[NH2] C=N[NH2] -37: smi match: C=NC=O C=NC=O -37: smi match: * * -37: smi match: C#NC C#NC -37: smi match: CN=C=O CN=C=O -37: smi match: CN=C=S CN=C=S -37: smi match: *OC(*)(*)O* *OC(*)(*)O* -37: smi match: *C(*)=O *C(*)=O -37: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C -37: smi match: *~*=O *~*=O -37: smi match: *~*=O *~*=O -37: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] -37: smi match: * * -37: smi match: *C#N *C#N -37: smi match: *N(=O)~O *N(=O)~O -37: smi match: N N -37: smi match: OC(=O)C(O)=O OC(=O)C(O)=O -37: smi match: C=NO C=NO -37: smi match: O~O O~O -37: smi match: c[OH] c[OH] -37: smi match: O=P(~[OH])~O O=P(~[OH])~O -37: smi match: CO~P(=O)~O CO~P(=O)~O -37: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O -37: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O -47: Randomness seeded to: 3963187520 +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [23:38:03] Unusual charge on atom 0 number of radical electrons set to zero +46: [23:38:03] Unusual charge on atom 0 number of radical electrons set to zero +46: [23:38:03] Unusual charge on atom 0 number of radical electrons set to zero +46: [23:38:03] non-ring atom 0 marked aromatic +47: Randomness seeded to: 1512794421 47: =============================================================================== 47: All tests passed (62 assertions in 6 test cases) 47: - 38/236 Test #47: graphmolOrganometallicsCatch ........... Passed 0.13 sec -46: [03:09:34] Explicit valence for atom # 1 O, 3, is greater than permitted -test 50 - Start 50: chiralityTestsCatch - -50: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/chiralityTestsCatch -50: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol -50: Test timeout computed to be: 1500 -46: [03:09:34] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [03:09:34] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [03:09:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [03:09:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [03:09:34] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. -46: [03:09:34] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom -46: [03:09:34] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom -46: [03:09:34] non-ring atom 0 marked aromatic -46: [03:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [03:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -37: smi match: O=P(~O)~O O=P(~O)~O -37: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O -37: smi match: C[NH2] C[NH2] -37: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 -37: smi match: * * -37: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 -37: smi match: CS(C)~O CS(C)~O -37: smi match: CS(C)(~O)~O CS(C)(~O)~O -37: smi match: CS(N)(~O)~O CS(N)(~O)~O -37: smi match: CS([OH])(~O)~O CS([OH])(~O)~O -37: smi match: COS(C)(~O)~O COS(C)(~O)~O -37: smi match: *S(C)(~O)~O *S(C)(~O)~O -37: smi match: CN(C)C CN(C)C -37: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 -37: smi match: *C(*)=S *C(*)=S -37: smi match: *OC(*)=S *OC(*)=S -37: smi match: * * -37: smi match: C[SH] C[SH] -37: smi match: c[SH] c[SH] -37: smi match: NC(N)=S NC(N)=S -37: smi match: * * -37: smi match: ***** ***** -37: smi match: NC(N)=O NC(N)=O -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing sf.net issue 280. -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing sf.net issue 285. -37: [03:09:34] done -37: [03:09:34] done -37: [03:09:34] done -37: [03:09:34] done -37: [03:09:34] done -37: [03:09:34] done -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing Github2441: Add RDProps interface to Conformers. -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing Issue2510: Pickle Confs as double. -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing loading pickled mols with conformers -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing conformer reading/writing options -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing property reading options -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing property reading options - 39/236 Test #32: pyDistGeom ............................. Passed 0.55 sec -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing boost::serialization integration -37: [03:09:34] done -37: [03:09:34] ------------------------------------- -37: [03:09:34] Testing github issue 6036 - 40/236 Test #37: graphmoltestPickler .................... Passed 0.41 sec + 39/236 Test #47: graphmolOrganometallicsCatch ........... Passed 0.07 sec test 51 Start 51: canonTestsCatch 51: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/canonTestsCatch 51: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 51: Test timeout computed to be: 1500 +46: [23:38:03] non-ring atom 0 marked aromatic +46: [23:38:03] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [23:38:03] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [23:38:03] Explicit valence for atom # 3 N, 4, is greater than permitted +46: [23:38:03] Explicit valence for atom # 15 C, 5, is greater than permitted +46: [23:38:03] Explicit valence for atom # 11 C, 5, is greater than permitted +46: [23:38:03] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [23:38:03] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [23:38:03] Explicit valence for atom # 9 C, 6, is greater than permitted +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 7 +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 3 +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 3 7 +46: [23:38:03] Can't kekulize mol. Unkekulized atoms: 3 7 +46: [23:38:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +48: Randomness seeded to: 3128950384 +48: =============================================================================== +48: All tests passed (136 assertions in 8 test cases) +48: + 40/236 Test #48: graphmolSGroupCatch .................... Passed 0.09 sec test 52 Start 52: moliteratorTestsCatch 52: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/moliteratorTestsCatch 52: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 52: Test timeout computed to be: 1500 -46: [03:09:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [03:09:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [03:09:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [03:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -46: [03:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -46: [03:09:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [03:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [03:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [03:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [03:09:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -40: [03:09:34] sorting (hanoi sort) vectors -49: Randomness seeded to: 1181884559 +46: [23:38:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +50: Randomness seeded to: 2980082202 +50: [23:38:03] unable to set wavy bonds for double bonds: 3 +50: [23:38:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +50: [23:38:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +49: Randomness seeded to: 3871187655 49: =============================================================================== 49: All tests passed (292 assertions in 12 test cases) 49: @@ -17739,172 +17751,197 @@ 53: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/queryTestsCatch 53: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 53: Test timeout computed to be: 1500 -50: Randomness seeded to: 3138877064 -50: [03:09:34] unable to set wavy bonds for double bonds: 3 -46: [03:09:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -50: [03:09:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -50: [03:09:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -52: Randomness seeded to: 3307690566 +40: [23:38:03] sorting (hanoi sort) vectors +52: Randomness seeded to: 3272107442 52: =============================================================================== 52: All tests passed (14 assertions in 4 test cases) 52: - 42/236 Test #52: moliteratorTestsCatch .................. Passed 0.08 sec + 42/236 Test #52: moliteratorTestsCatch .................. Passed 0.06 sec test 54 Start 54: molbundleTestsCatch 54: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/molbundleTestsCatch 54: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 54: Test timeout computed to be: 1500 -53: Randomness seeded to: 1990574921 +30: ...[23:38:03] Molecule does not have explicit Hs. Consider calling AddHs() +46: [23:38:03] Explicit valence for atom # 1 O, 3, is greater than permitted +46: [23:38:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [23:38:03] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [23:38:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [23:38:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [23:38:03] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. +46: [23:38:03] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom +46: [23:38:03] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom +46: [23:38:03] non-ring atom 0 marked aromatic +46: [23:38:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [23:38:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +50: [23:38:03] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +50: [23:38:03] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +50: [23:38:03] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +53: Randomness seeded to: 3675494153 53: =============================================================================== 53: All tests passed (10 assertions in 1 test case) 53: -50: [03:09:35] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -50: [03:09:35] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -50: [03:09:35] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored - 43/236 Test #53: queryTestsCatch ........................ Passed 0.08 sec + 43/236 Test #53: queryTestsCatch ........................ Passed 0.04 sec test 55 Start 55: pickleTestsCatch 55: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/pickleTestsCatch 55: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 55: Test timeout computed to be: 1500 -46: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [03:09:35] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [03:09:35] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [03:09:35] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [03:09:35] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [03:09:35] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [03:09:35] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [03:09:35] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [03:09:35] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [03:09:35] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [03:09:35] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [03:09:35] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [03:09:35] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [03:09:35] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [03:09:35] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [03:09:35] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [03:09:35] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [03:09:35] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [03:09:35] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [03:09:35] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: [03:09:35] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: =============================================================================== -46: All tests passed (4479 assertions in 107 test cases) -46: +46: [23:38:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 50: =============================================================================== 50: All tests passed (2295 assertions in 80 test cases) 50: -54: Randomness seeded to: 3036660380 -54: =============================================================================== -54: All tests passed (6 assertions in 1 test case) -54: - 44/236 Test #46: graphmolTestsCatch ..................... Passed 0.35 sec - 45/236 Test #50: chiralityTestsCatch .................... Passed 0.20 sec - 46/236 Test #54: molbundleTestsCatch .................... Passed 0.06 sec + 44/236 Test #50: chiralityTestsCatch .................... Passed 0.13 sec test 56 Start 56: tableTestsCatch 56: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/tableTestsCatch 56: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 56: Test timeout computed to be: 1500 +54: Randomness seeded to: 1152894207 +54: =============================================================================== +54: All tests passed (6 assertions in 1 test case) +54: +46: [23:38:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [23:38:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 45/236 Test #54: molbundleTestsCatch .................... Passed 0.05 sec test 57 Start 57: molopsTestsCatch 57: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/molopsTestsCatch 57: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol 57: Test timeout computed to be: 1500 +46: [23:38:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +46: [23:38:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +46: [23:38:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +56: Randomness seeded to: 1055950111 +56: =============================================================================== +56: All tests passed (7 assertions in 2 test cases) +56: + 46/236 Test #56: tableTestsCatch ........................ Passed 0.03 sec test 58 Start 58: smiTest1 58: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 58: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 58: Test timeout computed to be: 1500 -30: ......[03:09:35] Molecule does not have explicit Hs. Consider calling AddHs() -55: Randomness seeded to: 962941531 +46: [23:38:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [23:38:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [23:38:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [23:38:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [23:38:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +55: Randomness seeded to: 3632878352 55: =============================================================================== 55: All tests passed (45 assertions in 4 test cases) 55: -56: Randomness seeded to: 1597789842 -56: =============================================================================== -56: All tests passed (7 assertions in 2 test cases) -56: - 47/236 Test #55: pickleTestsCatch ....................... Passed 0.08 sec - 48/236 Test #56: tableTestsCatch ........................ Passed 0.06 sec + 47/236 Test #55: pickleTestsCatch ....................... Passed 0.06 sec test 59 Start 59: smiTest2 59: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 59: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 59: Test timeout computed to be: 1500 +57: Randomness seeded to: 3447446600 +57: =============================================================================== +57: All tests passed (230 assertions in 7 test cases) +57: + 48/236 Test #57: molopsTestsCatch ....................... Passed 0.05 sec test 60 Start 60: cxsmilesTest 60: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 60: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 60: Test timeout computed to be: 1500 -57: Randomness seeded to: 4183664777 -57: =============================================================================== -57: All tests passed (230 assertions in 7 test cases) -57: -59: [03:09:35] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -59: [03:09:35] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [03:09:35] SMILES Parse Error: syntax error while parsing: - -59: [03:09:35] SMILES Parse Error: check for mistakes around position 1: -59: [03:09:35] - -59: [03:09:35] ^ -59: [03:09:35] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -59: [03:09:35] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -59: [03:09:35] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -59: [03:09:35] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [03:09:35] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -59: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -59: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -59: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -59: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -59: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -59: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -59: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 49/236 Test #57: molopsTestsCatch ....................... Passed 0.07 sec - 50/236 Test #59: smiTest2 ............................... Passed 0.03 sec -58: [03:09:35] WARNING: not removing hydrogen atom without neighbors -58: [03:09:35] WARNING: not removing hydrogen atom without neighbors +59: [23:38:03] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +59: [23:38:03] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [23:38:03] SMILES Parse Error: syntax error while parsing: - +59: [23:38:03] SMILES Parse Error: check for mistakes around position 1: +59: [23:38:03] - +59: [23:38:03] ^ +59: [23:38:03] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +59: [23:38:03] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +59: [23:38:03] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +59: [23:38:03] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [23:38:03] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +59: [23:38:03] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +59: [23:38:03] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +59: [23:38:03] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +59: [23:38:03] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +59: [23:38:03] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +59: [23:38:03] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +59: [23:38:03] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' +58: [23:38:03] WARNING: not removing hydrogen atom without neighbors +58: [23:38:03] WARNING: not removing hydrogen atom without neighbors +58: [23:38:03] WARNING: not removing hydrogen atom without neighbors +58: [23:38:03] WARNING: not removing hydrogen atom without neighbors +58: [23:38:03] WARNING: not removing hydrogen atom without neighbors +58: [23:38:03] WARNING: not removing hydrogen atom without neighbors +58: [23:38:03] WARNING: not removing hydrogen atom without neighbors +58: [23:38:03] WARNING: not removing hydrogen atom without neighbors +58: [23:38:03] WARNING: not removing hydrogen atom without neighbors +58: [23:38:03] WARNING: not removing hydrogen atom without neighbors + 49/236 Test #59: smiTest2 ............................... Passed 0.03 sec test 61 Start 61: smaTest1 61: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 61: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 61: Test timeout computed to be: 1500 +58: [23:38:03] WARNING: not removing hydrogen atom without neighbors +58: [23:38:03] Invalid chiral specification on atom 0 +58: [23:38:03] Invalid chiral specification on atom 0 +58: [23:38:03] Invalid chiral specification on atom 0 +58: [23:38:03] Invalid chiral specification on atom 0 +58: [23:38:03] Invalid chiral specification on atom 0 +46: [23:38:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [23:38:03] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [23:38:03] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [23:38:03] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [23:38:03] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [23:38:03] Explicit valence for atom # 0 P, 6, is greater than permitted +46: [23:38:03] Explicit valence for atom # 0 P, 6, is greater than permitted +46: [23:38:03] Explicit valence for atom # 0 P, 7, is greater than permitted +46: [23:38:03] Explicit valence for atom # 0 P, 7, is greater than permitted +46: [23:38:03] Explicit valence for atom # 1 As, 6, is greater than permitted +46: [23:38:03] Explicit valence for atom # 1 As, 6, is greater than permitted +46: [23:38:03] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [23:38:03] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [23:38:03] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [23:38:03] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [23:38:03] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [23:38:03] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [23:38:03] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [23:38:03] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [23:38:03] Explicit valence for atom # 1 Bi, 8, is greater than permitted +46: [23:38:03] Explicit valence for atom # 1 Bi, 8, is greater than permitted +46: =============================================================================== +46: All tests passed (4479 assertions in 107 test cases) +46: + 50/236 Test #46: graphmolTestsCatch ..................... Passed 0.31 sec +58: [23:38:03] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +58: [23:38:03] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' test 62 Start 62: smiTestCatch 62: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 62: Test timeout computed to be: 1500 -58: [03:09:35] WARNING: not removing hydrogen atom without neighbors -58: [03:09:35] WARNING: not removing hydrogen atom without neighbors -58: [03:09:35] WARNING: not removing hydrogen atom without neighbors -58: [03:09:35] WARNING: not removing hydrogen atom without neighbors -58: [03:09:35] WARNING: not removing hydrogen atom without neighbors -58: [03:09:35] WARNING: not removing hydrogen atom without neighbors -58: [03:09:35] WARNING: not removing hydrogen atom without neighbors -58: [03:09:35] WARNING: not removing hydrogen atom without neighbors -58: [03:09:35] WARNING: not removing hydrogen atom without neighbors -58: [03:09:35] Invalid chiral specification on atom 0 -58: [03:09:35] Invalid chiral specification on atom 0 -58: [03:09:35] Invalid chiral specification on atom 0 -58: [03:09:35] Invalid chiral specification on atom 0 -58: [03:09:35] Invalid chiral specification on atom 0 -58: [03:09:35] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -58: [03:09:35] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -35: [03:09:35] Maximum BFS search size exceeded. -35: This is likely due to a highly symmetric fused ring system. +62: Randomness seeded to: 2963914901 +62: [23:38:03] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +62: [23:38:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [23:38:03] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +62: [23:38:03] SMARTS Parse Error: unclosed ring for input: 'C1C' +62: [23:38:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [23:38:03] SMARTS Parse Error: syntax error while parsing: C)foo +62: [23:38:03] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +62: [23:38:03] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +62: [23:38:03] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +62: [23:38:03] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' 58: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -62: Randomness seeded to: 3162350307 -62: [03:09:35] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -62: [03:09:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -62: [03:09:35] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +62: [23:38:04] w block attempts to set wedging on bond 0 more than once. +62: [23:38:04] improperly formatted w block 58: smi: ClC1CCCCC1 58: smi: ClC1CCCCC1 58: smi: ClC1CCCCC1Br @@ -17913,120 +17950,16 @@ 58: smi: c1cc[nH]c1 58: smi: c1cc[nH]c1 58: smi: c1cc[pH]c1 -58: [03:09:35] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -58: [03:09:35] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -62: [03:09:35] SMARTS Parse Error: unclosed ring for input: 'C1C' -62: [03:09:35] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -62: [03:09:35] SMARTS Parse Error: syntax error while parsing: C)foo -62: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -62: [03:09:35] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -62: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -62: [03:09:35] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +62: [23:38:04] atom 3 is not associated with bond 1(1-2) in w block +58: [23:38:04] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: [23:38:04] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 58: CbC(aC)aC 58: CaC(bC)aC 58: CbC(bC)aC 58: O.C +30: ......[23:38:04] Molecule does not have explicit Hs. Consider calling AddHs() 58: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O -58: [03:09:35] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -58: [03:09:35] SMILES Parse Error: check for mistakes around position 4: -58: [03:09:35] c%()ccccc%() -58: [03:09:35] ~~~^ -58: [03:09:35] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -58: [03:09:35] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -58: [03:09:35] SMILES Parse Error: check for mistakes around position 9: -58: [03:09:35] c%(100000)ccccc%(100000) -58: [03:09:35] ~~~~~~~~^ -58: [03:09:35] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -58: [03:09:35] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -58: [03:09:35] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -58: [03:09:35] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [03:09:35] SMILES Parse Error: check for mistakes around position 14: -58: [03:09:35] COc(c1)cccc1C# -58: [03:09:35] ~~~~~~~~~~~~~^ -58: [03:09:35] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [03:09:35] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [03:09:35] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [03:09:35] SMILES Parse Error: check for mistakes around position 14: -58: [03:09:35] COc(c1)cccc1C# -58: [03:09:35] ~~~~~~~~~~~~~^ -58: [03:09:35] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [03:09:35] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [03:09:35] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [03:09:35] SMILES Parse Error: check for mistakes around position 14: -58: [03:09:35] COc(c1)cccc1C# -58: [03:09:35] ~~~~~~~~~~~~~^ -58: [03:09:35] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [03:09:35] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: C=c1s/c2n(c1=O)CCCCCCC\N=2 -58: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -58: [03:09:35] SMILES Parse Error: extra close parentheses while parsing: C) -58: [03:09:35] SMILES Parse Error: check for mistakes around position 2: -58: [03:09:35] C) -58: [03:09:35] ~^ -58: [03:09:35] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' - 51/236 Test #58: smiTest1 ............................... Passed 0.14 sec -test 63 - Start 63: nontetrahedralCatch - -63: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch -63: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse -63: Test timeout computed to be: 1500 -61: [03:09:35] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -61: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -61: [03:09:35] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -61: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -61: [03:09:35] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -61: [03:09:35] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -30: ... -30: ---------------------------------------------------------------------- -30: Ran 12 tests in 0.624s -30: -30: OK - 52/236 Test #61: smaTest1 ............................... Passed 0.15 sec -test 64 - Start 64: v2smiTestCatch - -64: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch -64: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse -64: Test timeout computed to be: 1500 -62: [03:09:35] w block attempts to set wedging on bond 0 more than once. -62: [03:09:35] improperly formatted w block -62: [03:09:35] atom 3 is not associated with bond 1(1-2) in w block -62: [03:09:35] -62: -62: **** -62: Range Error -62: idx -62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -62: Failed Expression: 20 < 20 -62: ---------- -62: Stacktrace: -62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 7# 0x0000AAAAE9B79F8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000AAAAE9BCA9EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000AAAAE9BCB3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000AAAAE9BCB7D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000AAAAE9B9FB98 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000AAAAE9BA00E4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000AAAAE9B357D0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x0000FFFF926A229C in /lib/aarch64-linux-gnu/libc.so.6 -62: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -62: 16# 0x0000AAAAE9B358B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: ---------- -62: **** -62: -63: Randomness seeded to: 140756399 -63: [03:09:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -60: Randomness seeded to: 2445505577 +60: Randomness seeded to: 149855353 60: Test 60: 60: ShortAtropisomerNoCoords.cxsmi @@ -18087,13 +18020,64 @@ 60: 60: BMS-986142_atrop5.cxsmi 60: -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -62: [03:09:35] +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +58: [23:38:04] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +58: [23:38:04] SMILES Parse Error: check for mistakes around position 4: +58: [23:38:04] c%()ccccc%() +58: [23:38:04] ~~~^ +58: [23:38:04] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +58: [23:38:04] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +58: [23:38:04] SMILES Parse Error: check for mistakes around position 9: +58: [23:38:04] c%(100000)ccccc%(100000) +58: [23:38:04] ~~~~~~~~^ +58: [23:38:04] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +58: [23:38:04] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +58: [23:38:04] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +58: [23:38:04] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [23:38:04] SMILES Parse Error: check for mistakes around position 14: +58: [23:38:04] COc(c1)cccc1C# +58: [23:38:04] ~~~~~~~~~~~~~^ +58: [23:38:04] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [23:38:04] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [23:38:04] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [23:38:04] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [23:38:04] SMILES Parse Error: check for mistakes around position 14: +58: [23:38:04] COc(c1)cccc1C# +58: [23:38:04] ~~~~~~~~~~~~~^ +58: [23:38:04] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [23:38:04] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [23:38:04] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [23:38:04] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [23:38:04] SMILES Parse Error: check for mistakes around position 14: +58: [23:38:04] COc(c1)cccc1C# +58: [23:38:04] ~~~~~~~~~~~~~^ +58: [23:38:04] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [23:38:04] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [23:38:04] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: C=c1s/c2n(c1=O)CCCCCCC\N=2 +58: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 +58: [23:38:04] SMILES Parse Error: extra close parentheses while parsing: C) +58: [23:38:04] SMILES Parse Error: check for mistakes around position 2: +58: [23:38:04] C) +58: [23:38:04] ~^ +58: [23:38:04] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' + 51/236 Test #58: smiTest1 ............................... Passed 0.28 sec +test 63 + Start 63: nontetrahedralCatch + +63: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch +63: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse +63: Test timeout computed to be: 1500 +62: [23:38:04] 62: 62: **** 62: Range Error @@ -18109,43 +18093,60 @@ 62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 7# 0x0000AAAAE9B79F8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000AAAAE9BCA9EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000AAAAE9BCB3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000AAAAE9BCB7D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000AAAAE9B9FB98 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000AAAAE9BA00E4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000AAAAE9B357D0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x0000FFFF926A229C in /lib/aarch64-linux-gnu/libc.so.6 +62: 7# 0x0000AAAAE9169F8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x0000AAAAE91BA9EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x0000AAAAE91BB3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x0000AAAAE91BB7D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x0000AAAAE918FB98 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x0000AAAAE91900E4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x0000AAAAE91257D0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x0000FFFF9C34229C in /lib/aarch64-linux-gnu/libc.so.6 62: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -62: 16# 0x0000AAAAE9B358B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 16# 0x0000AAAAE91258B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: ---------- 62: **** 62: -62: [03:09:35] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [03:09:35] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [03:09:35] SMARTS Parse Error: syntax error while parsing: C1C)foo -62: [03:09:35] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' -62: [03:09:35] SMILES Parse Error: extra close parentheses while parsing: C1C)foo -62: [03:09:35] SMILES Parse Error: check for mistakes around position 4: -62: [03:09:35] C1C)foo -62: [03:09:35] ~~~^ -62: [03:09:35] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' -64: Randomness seeded to: 1530089511 -64: =============================================================================== -64: All tests passed (14 assertions in 2 test cases) -64: - 53/236 Test #64: v2smiTestCatch ......................... Passed 0.03 sec -test 65 - Start 65: testDepictor - -65: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/testDepictor -65: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor -65: Test timeout computed to be: 1500 -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +62: [23:38:04] +62: +62: **** +62: Range Error +62: idx +62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +62: Failed Expression: 20 < 20 +62: ---------- +62: Stacktrace: +62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 7# 0x0000AAAAE9169F8C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x0000AAAAE91BA9EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x0000AAAAE91BB3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x0000AAAAE91BB7D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x0000AAAAE918FB98 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x0000AAAAE91900E4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x0000AAAAE91257D0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x0000FFFF9C34229C in /lib/aarch64-linux-gnu/libc.so.6 +62: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +62: 16# 0x0000AAAAE91258B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: ---------- +62: **** +62: +62: [23:38:04] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [23:38:04] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [23:38:04] SMARTS Parse Error: syntax error while parsing: C1C)foo +62: [23:38:04] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' +62: [23:38:04] SMILES Parse Error: extra close parentheses while parsing: C1C)foo +62: [23:38:04] SMILES Parse Error: check for mistakes around position 4: +62: [23:38:04] C1C)foo +62: [23:38:04] ~~~^ +62: [23:38:04] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' +62: =============================================================================== +62: All tests passed (1588 assertions in 69 test cases) +62: 60: Test 60: 60: BMS-986142_atrop6.cxsmi @@ -18154,42 +18155,65 @@ 60: 60: BMS-986142_atropBad1.cxsmi 60: -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -62: =============================================================================== -62: All tests passed (1588 assertions in 69 test cases) -62: - 54/236 Test #62: smiTestCatch ........................... Passed 0.17 sec -test 66 - Start 66: depictorCatch - -66: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/depictorCatch -66: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor -66: Test timeout computed to be: 1500 -63: [03:09:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 60: Test 60: 60: BMS-986142_atropBad2.cxsmi 60: -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -63: [03:09:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [03:09:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [03:09:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [03:09:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [03:09:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [03:09:35] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [03:09:35] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +61: [23:38:04] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +61: [23:38:04] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +61: [23:38:04] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +61: [23:38:04] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +61: [23:38:04] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +61: [23:38:04] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged + 52/236 Test #62: smiTestCatch ........................... Passed 0.22 sec +test 64 + Start 64: v2smiTestCatch + +64: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch +64: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse +64: Test timeout computed to be: 1500 +63: Randomness seeded to: 2505394648 +63: [23:38:04] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [23:38:04] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry + 53/236 Test #61: smaTest1 ............................... Passed 0.26 sec +test 65 + Start 65: testDepictor + +65: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/testDepictor +65: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor +65: Test timeout computed to be: 1500 +63: [23:38:04] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [23:38:04] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [23:38:04] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [23:38:04] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [23:38:04] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [23:38:04] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [23:38:04] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. 63: =============================================================================== 63: All tests passed (308 assertions in 9 test cases) 63: - 55/236 Test #63: nontetrahedralCatch .................... Passed 0.18 sec + 54/236 Test #63: nontetrahedralCatch .................... Passed 0.05 sec +test 66 + Start 66: depictorCatch + +66: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/depictorCatch +66: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Depictor +66: Test timeout computed to be: 1500 +64: Randomness seeded to: 3716312003 +64: =============================================================================== +64: All tests passed (14 assertions in 2 test cases) +64: + 55/236 Test #64: v2smiTestCatch ......................... Passed 0.04 sec test 67 Start 67: pyDepictor @@ -18220,11 +18244,13 @@ 60: 60: JDQ443_atropBad1.cxsmi 60: -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +35: [23:38:04] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. 60: Test 60: 60: RP-6306_atrop1.cxsmi @@ -18245,23 +18271,16 @@ 60: 60: RP-6306_atrop5.cxsmi 60: -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored - 56/236 Test #30: pyForceFieldConstraints ................ Passed 1.28 sec -test 68 - Start 68: testMrvToMol - -68: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse -68: Test timeout computed to be: 1500 +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 60: Test 60: 60: RP-6306_atrop6.cxsmi @@ -18270,26 +18289,31 @@ 60: 60: RP-6306_atropBad1.cxsmi 60: -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 60: Test 60: 60: RP-6306_atropBad2.cxsmi 60: -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -66: Randomness seeded to: 428526969 +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +66: Randomness seeded to: 1950693823 66: =============================================================================== 66: All tests passed (580 assertions in 18 test cases) 66: -65: [03:09:35] Warning: stereochemistry around double bond may be incorrect in depiction. - 57/236 Test #66: depictorCatch .......................... Passed 0.19 sec + 56/236 Test #66: depictorCatch .......................... Passed 0.09 sec +test 68 + Start 68: testMrvToMol + +68: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse +68: Test timeout computed to be: 1500 60: Test 60: 60: RP-6306_3d.cxsmi @@ -18314,52 +18338,34 @@ 60: 60: Sotorasib_atrop5.cxsmi 60: -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -test 69 - Start 69: fileParsersTest1 - -69: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -69: Test timeout computed to be: 1500 -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored 60: Test 60: 60: Sotorasib_atropBad1.cxsmi 60: -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 60: Test 60: 60: Sotorasib_atropBad2.cxsmi 60: -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -69: *************************************** -69: *************************************** - 58/236 Test #65: testDepictor ........................... Passed 0.26 sec -test 70 - Start 70: testAtropisomers - -70: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers -70: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -70: Test timeout computed to be: 1500 -69: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [03:09:35] bond with order 0 found on line 7. This is not part of the MDL specification. +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 68: Using new chirality perception 68: Test 68: @@ -18369,13 +18375,12 @@ 68: 68: 145323811.mol 68: -68: [03:09:35] unsupported number of radical electrons 5 -69: [03:09:35] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [03:09:35] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [03:09:35] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -69: generating smiles -69: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -69: converting back +68: [23:38:04] unsupported number of radical electrons 5 +30: ... +30: ---------------------------------------------------------------------- +30: Ran 12 tests in 0.666s +30: +30: OK 60: Test 60: 60: Sotorasib_3d.cxsmi @@ -18400,13 +18405,11 @@ 60: 60: ZM374979_atropBad1.cxsmi 60: -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [03:09:35] ---- Running with POSIX locale ----- -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -69: check isomorphism +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 68: Test 68: 68: NewChiralTest.sdf @@ -18439,15 +18442,8 @@ 68: 68: ProblemShort.mol 68: -68: [03:09:35] For a MultipleSgroup expansion, the matching orphaned bond was not found +68: [23:38:04] For a MultipleSgroup expansion, the matching orphaned bond was not found 68: The multiple sgroup will be ignored -35: [03:09:35] Maximum BFS search size exceeded. -35: This is likely due to a highly symmetric fused ring system. -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 60: Test 60: 60: Mrtx1719_3d.cxsmi @@ -18472,373 +18468,23 @@ 60: 60: Mrtx1719_atropBad1.cxsmi 60: -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -35: F/C=C/Cl -35: [H]/C(F)=C(/[H])Cl -35: F/C=C/Cl -35: F/C=C/Cl -35: C/C(F)=C(/C)Cl -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -35: [03:09:35] ----------------------- -35: Testing isRingFused -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 - 59/236 Test #35: graphmolMolOpsTest ..................... Passed 1.32 sec -test 71 - Start 71: testSquiggleDoubleBonds - -71: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds -71: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -71: Test timeout computed to be: 1500 -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [03:09:35] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: Randomness seeded to: 89385214 -71: =============================================================================== -71: All tests passed (15 assertions in 3 test cases) -71: - 60/236 Test #71: testSquiggleDoubleBonds ................ Passed 0.05 sec -test 72 - Start 72: testMolSupplier - -72: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -72: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -72: Test timeout computed to be: 1500 -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [03:09:35] -72: ----------------------------------------- -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [03:09:35] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -72: [03:09:35] Ignoring invalid chirality label: '2_bad_chirality' -72: [03:09:35] Finished: testMolSup() -72: [03:09:35] ----------------------------------------- -72: -72: [03:09:35] ----------------------------------------- -72: [03:09:35] Finished: testRandMolSup() -72: [03:09:35] ----------------------------------------- -72: -72: [03:09:35] ----------------------------------------- -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:09:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: Atropisomers- 1 hits 3 misses -70: Final results: -70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses - 61/236 Test #70: testAtropisomers ....................... Passed 0.38 sec -test 73 - Start 73: testGeneralFileReader - -73: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -73: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -73: Test timeout computed to be: 1500 -72: [03:09:35] Finished: testSmilesSup() -72: [03:09:35] ----------------------------------------- -72: -72: [03:09:35] ----------------------------------------- -72: [03:09:35] ------------------------------------------------------ -72: [03:09:35] SMILES Parse Error: syntax error while parsing: fail -72: [03:09:35] SMILES Parse Error: check for mistakes around position 1: -72: [03:09:35] fail -72: [03:09:35] ^ -72: [03:09:35] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -72: [03:09:35] ERROR: Smiles parse error on line 3 -72: [03:09:35] ERROR: Cannot create molecule from : 'fail' -72: [03:09:35] ------------------------------------------------------ -72: [03:09:35] ------------------------------------------------------ -72: [03:09:35] >>> This may result in an infinite loop. It should finish almost immediately: -72: [03:09:35] <<< done. -72: [03:09:35] Finished: testSmilesSupFromText() -72: [03:09:35] ----------------------------------------- -72: -72: [03:09:35] ----------------------------------------- -72: [03:09:35] Finished: testSmilesWriter() -72: [03:09:35] ----------------------------------------- -72: -72: [03:09:35] ----------------------------------------- -72: [03:09:36] Finished: testSDWriter() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testSDSupplierEnding() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testSuppliersEmptyFile() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testCisTrans() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -73: [03:09:36] -73: ----------------------------------------- -73: [03:09:36] Finished: testDetermineFormat() -73: [03:09:36] ----------------------------------------- -73: -73: [03:09:36] -73: ----------------------------------------- -72: [03:09:36] Finished: testStereoRound() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [03:09:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [03:09:36] Finished: testIssue226() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testTDTSupplier1() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testTDTSupplier2() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testTDTSupplier3() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testSDSupplierFromText() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] ERROR: Problems encountered parsing data fields -72: [03:09:36] ERROR: moving to the beginning of the next molecule -72: [03:09:36] ERROR: Problems encountered parsing data fields -72: [03:09:36] ERROR: moving to the beginning of the next molecule -72: [03:09:36] Spurious data before the first property will be ignored -72: [03:09:36] Property will be truncated after the first blank line -72: [03:09:36] Property will be truncated after the first blank line -72: [03:09:36] Property will be truncated after the first blank line -72: [03:09:36] Finished: testSDSupplierStrLax1() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] ERROR: Problems encountered parsing data fields -72: [03:09:36] ERROR: moving to the beginning of the next molecule -72: [03:09:36] Property will be truncated after the first blank line -72: [03:09:36] Finished: testSDSupplierStrLax2() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] ERROR: Problems encountered parsing data fields -72: [03:09:36] ERROR: moving to the beginning of the next molecule -72: [03:09:36] ERROR: Problems encountered parsing data fields -72: [03:09:36] ERROR: moving to the beginning of the next molecule -72: [03:09:36] Spurious data before the first property will be ignored -72: [03:09:36] Property will be truncated after the first blank line -72: [03:09:36] Property will be truncated after the first blank line -72: [03:09:36] Property will be truncated after the first blank line -72: [03:09:36] Finished: testSDSupplierFromTextStrLax1() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] ERROR: Problems encountered parsing data fields -72: [03:09:36] ERROR: moving to the beginning of the next molecule -72: [03:09:36] Property will be truncated after the first blank line -72: [03:09:36] Finished: testSDSupplierFromTextStrLax2() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testIssue265() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] ERROR: End of data field name not found -72: [03:09:36] ERROR: moving to the beginning of the next molecule -72: [03:09:36] Explicit valence for atom # 0 F, 2, is greater than permitted -72: [03:09:36] ERROR: Could not sanitize molecule ending on line 16 -72: [03:09:36] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -72: [03:09:36] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -72: [03:09:36] ERROR: moving to the beginning of the next molecule -72: [03:09:36] ERROR: Bond line too short: 'M END' on line 18 -72: [03:09:36] ERROR: moving to the beginning of the next molecule -72: [03:09:36] Finished: testSDErrorHandling() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testIssue381() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testSetStreamIndices() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testMixIterAndRandom() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: build: -72: [03:09:36] Finished: testRemoveHs() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testGetItemText() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testForwardSDSupplier() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testMissingCRSDSupplier() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testIssue3482695() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] ERROR: Cannot convert 'foo' to unsigned int on line 557 -72: [03:09:36] ERROR: moving to the beginning of the next molecule -72: [03:09:36] Finished: testIssue3525673() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testBlankLinesInProps() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testSkipLines() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testGitHub23() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testGitHub88() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -73: [03:09:36] Finished: testSdf() -73: [03:09:36] ----------------------------------------- -73: -73: [03:09:36] -73: ----------------------------------------- -72: [03:09:36] Finished: testGitHub2285() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -72: [03:09:36] ERROR: Smiles parse error on line 1 -72: [03:09:36] ERROR: Cannot create molecule from : 'c1ccccc' -72: [03:09:36] SMILES Parse Error: extra open parentheses while parsing: C(C -72: [03:09:36] SMILES Parse Error: check for mistakes around position 2: -72: [03:09:36] C(C -72: [03:09:36] ~^ -72: [03:09:36] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -72: [03:09:36] ERROR: Smiles parse error on line 3 -72: [03:09:36] ERROR: Cannot create molecule from : 'C(C' -72: [03:09:36] Explicit valence for atom # 1 C, 5, is greater than permitted -72: [03:09:36] ERROR: Could not sanitize molecule on line 5 -72: [03:09:36] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -72: [03:09:36] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:09:36] ERROR: Could not sanitize molecule ending on line 21 -72: [03:09:36] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:09:36] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:09:36] ERROR: Could not sanitize molecule ending on line 21 -72: [03:09:36] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:09:36] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:09:36] ERROR: Could not sanitize molecule ending on line 21 -72: [03:09:36] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:09:36] ERROR: Atom line too short: ' -9.6' on line 28 -72: [03:09:36] ERROR: moving to the beginning of the next molecule -72: [03:09:36] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:09:36] ERROR: Could not sanitize molecule ending on line 21 -72: [03:09:36] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:09:36] ERROR: Atom line too short: ' -9.6' on line 28 -72: [03:09:36] ERROR: moving to the beginning of the next molecule -72: [03:09:36] Finished: testGitHub2479() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Ignoring invalid chirality label: '7_S_8_9_6_10' -72: [03:09:36] Finished: testGitHub2881() -72: [03:09:36] ----------------------------------------- -72: -72: [03:09:36] ----------------------------------------- -72: [03:09:36] Finished: testGitHub3517() -72: [03:09:36] ----------------------------------------- -72: - 62/236 Test #72: testMolSupplier ........................ Passed 0.26 sec -test 74 - Start 74: testMultithreadedMolSupplier +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 + 57/236 Test #30: pyForceFieldConstraints ................ Passed 1.38 sec +test 69 + Start 69: fileParsersTest1 -74: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier -74: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -74: Test timeout computed to be: 1500 -73: [03:09:36] Finished: testSmi() -73: [03:09:36] ----------------------------------------- -73: -73: [03:09:36] -73: ----------------------------------------- -74: [03:09:36] -74: ----------------------------------------- +69: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +69: Test timeout computed to be: 1500 +69: *************************************** +69: *************************************** +69: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:38:04] bond with order 0 found on line 7. This is not part of the MDL specification. 68: Test 68: 68: badWedgeError.sdf @@ -19151,23 +18797,11 @@ 68: 68: MulticenterSgroup.mrv 68: -68: [03:09:36] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -68: [03:09:36] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -73: [03:09:36] Finished: testMae() -73: [03:09:36] ----------------------------------------- -73: -73: [03:09:36] -73: ----------------------------------------- -73: [03:09:36] Finished: testTdt() -73: [03:09:36] ----------------------------------------- -73: - 63/236 Test #73: testGeneralFileReader .................. Passed 0.21 sec -test 75 - Start 75: testMolWriter - -75: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter -75: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -75: Test timeout computed to be: 1500 +68: [23:38:04] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +68: [23:38:04] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +69: [23:38:04] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [23:38:04] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +69: [23:38:04] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 68: Test 68: 68: GenericSgroup.mrv @@ -19200,7 +18834,7 @@ 68: 68: MarvinBadMissingMolID.mrv 68: -68: [03:09:36] +68: [23:38:04] 68: 68: **** 68: Test Assert @@ -19211,12 +18845,12 @@ 68: Stacktrace: 68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 2# 0x0000AAAAC058AC5C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 3# 0x0000AAAAC0595D5C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 4# 0x0000AAAAC0584918 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 5# 0x0000FFFFB968229C in /lib/aarch64-linux-gnu/libc.so.6 +68: 2# 0x0000AAAABC1DAC5C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 3# 0x0000AAAABC1E5D5C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 4# 0x0000AAAABC1D4918 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 5# 0x0000FFFFAAEE229C in /lib/aarch64-linux-gnu/libc.so.6 68: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -68: 7# 0x0000AAAAC0584B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 7# 0x0000AAAABC1D4B70 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 68: ---------- 68: **** 68: @@ -19301,6 +18935,9 @@ 68: MarvinBadSruAtomRef.mrv 68: 68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +69: generating smiles +69: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 +69: converting back 68: Test 68: 68: MarvinBadSruConnect.mrv @@ -19341,21 +18978,19 @@ 68: MarvinBadSupMissingAttachBond.mrv 68: 68: No attachment point found for bond to the condensed atom in a superatomSgroup +35: [23:38:04] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. 68: Test 68: 68: MarvinBadSupMissingAttachOrder.mrv 68: 68: Expected atom, order and bond, for an AttachmentPoint definition in MRV file -67: ..............[03:09:36] SMILES Parse Error: syntax error while parsing: invalidsmiles -67: [03:09:36] SMILES Parse Error: check for mistakes around position 1: -67: [03:09:36] invalidsmiles -67: [03:09:36] ^ -67: [03:09:36] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' -67: ..... -67: ---------------------------------------------------------------------- -67: Ran 19 tests in 0.456s -67: -67: OK +69: check isomorphism +35: F/C=C/Cl +35: [H]/C(F)=C(/[H])Cl +35: F/C=C/Cl +35: F/C=C/Cl +35: C/C(F)=C(/C)Cl 68: Test 68: 68: marvin03.mrv @@ -19420,8 +19055,8 @@ 68: 68: BMS-986142_atrop5.mrv 68: -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: 68: BMS-986142_atrop6.mrv @@ -19434,44 +19069,15 @@ 68: 68: BMS-986142_atrop8.mrv 68: -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -75: [03:09:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -75: 0.40201265 0.40201265 -75: -0.13299436 -0.13299436 -75: 1.00000017 1.00000017 -75: 0.8762226 0.8762226 -75: 0.9973909 0.9973909 -75: 1.00000003 1.00000003 -75: 0.36613799 0.36613799 -75: 2.1107185 2.1107185 -75: 0.99999982 0.99999982 -75: 2.48696157 2.48696157 -75: 1.00479935 1.00479935 -75: 0.99999999 0.99999999 -75: 3.03311841 3.03311841 -75: 2.23739955 2.23739955 -75: 1.0000001 1.0000001 -75: 3.00772337 3.00772337 -75: 0.37399294 0.37399294 -75: 2.07713325 2.07713325 -75: 3.0077234 3.0077234 -75: 0.37399312 0.37399312 -75: -0.07713336 -0.07713336 -75: [03:09:36] bond with order 0 found on line 11. This is not part of the MDL specification. -75: [03:09:36] bond with order 0 found on line 16. This is not part of the MDL specification. +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: 68: BMS-986142_atropBad2.mrv 68: -68: [03:09:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 - 64/236 Test #75: testMolWriter .......................... Passed 0.28 sec -test 76 - Start 76: testTplParser - -76: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testTplParser -76: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -76: Test timeout computed to be: 1500 +68: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +35: [23:38:04] ----------------------- +35: Testing isRingFused 68: Test 68: 68: JDQ443_3d.mrv @@ -19492,14 +19098,14 @@ 68: 68: JDQ443_atropBad1.mrv 68: -68: [03:09:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 - 65/236 Test #76: testTplParser .......................... Passed 0.04 sec -test 77 - Start 77: testMol2ToMol +68: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 + 58/236 Test #35: graphmolMolOpsTest ..................... Passed 1.24 sec +test 70 + Start 70: testAtropisomers -77: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol -77: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -77: Test timeout computed to be: 1500 +70: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers +70: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +70: Test timeout computed to be: 1500 68: Test 68: 68: RP-6306_atrop1.mrv @@ -19520,28 +19126,875 @@ 68: 68: RP-6306_atrop5.mrv 68: -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: Test 68: 68: RP-6306_atropBad1.mrv 68: -68: [03:09:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 - 66/236 Test #67: pyDepictor ............................. Passed 1.11 sec +68: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 68: Test 68: 68: RP-6306_atropBad2.mrv 68: -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [23:38:04] ---- Running with POSIX locale ----- +68: Test +68: +68: RP-6306_3d.mrv +68: +68: Test +68: +68: Sotorasib_atrop1.mrv +68: +68: Test +68: +68: Sotorasib_atrop2.mrv +68: +68: Test +68: +68: Sotorasib_atrop3.mrv +68: +68: Test +68: +68: Sotorasib_atrop4.mrv +68: +68: Test +68: +68: Sotorasib_atrop5.mrv +68: +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: Test +68: +68: Sotorasib_atropBad1.mrv +68: +68: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +68: Test +68: +68: Sotorasib_atropBad2.mrv +68: +68: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +65: [23:38:04] Warning: stereochemistry around double bond may be incorrect in depiction. +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: Test +68: +68: Sotorasib_3d.mrv +68: +68: Test +68: +68: ZM374979_atrop1.mrv +68: +68: Test +68: +68: ZM374979_atrop2.mrv +68: +68: Test +68: +68: ZM374979_atrop3.mrv +68: +68: Test +68: +68: ZM374979_atropBad1.mrv +68: +68: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: mrtx1719_3d.mrv +68: +68: Test +68: +68: mrtx1719_atrop1.mrv +68: +68: Test +68: +68: mrtx1719_atrop2.mrv +68: +68: Test +68: +68: mrtx1719_atrop3.mrv +68: +68: Test +68: +68: mrtx1719_atropBad1.mrv +68: +68: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: Test +60: +60: AtropCanon1.cxsmi +60: +60: Test +60: +60: AtropCanon2.cxsmi +60: +60: Test +60: +60: AtropCanon3.cxsmi +60: +60: Test +60: +60: BMS-986142_3d_chiral.cxsmi +60: +60: Test +60: +60: BMS-986142_3d.cxsmi +60: +60: =============================================================================== +60: All tests passed (2496 assertions in 31 test cases) +60: + 59/236 Test #60: cxsmilesTest ........................... Passed 0.92 sec +test 71 + Start 71: testSquiggleDoubleBonds + +71: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds +71: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +71: Test timeout computed to be: 1500 +68: Test +68: +68: FalseAtropisomer.mrv +68: +68: Test +68: +68: AtropEnhancedStereo.mrv +68: +68: Test +68: +68: AtropManyChirals.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced2.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced3.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced4.mrv +68: +68: Test +68: +68: BMS-986142_3d_chiral.mrv +68: +68: Test +68: +68: BMS-986142_3d.mrv +68: +68: Test +68: +68: BMS-986142_atrop1.mrv +68: +68: Test +68: +68: BMS-986142_atrop2.mrv +68: +68: Test +68: +68: BMS-986142_atrop3.mrv +68: +68: Test +68: +68: BMS-986142_atrop4.mrv +68: +68: Test +68: +68: BMS-986142_atrop5.mrv +68: +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +68: Test +68: +68: BMS-986142_atrop6.mrv +68: +68: Test +68: +68: BMS-986142_atrop7.mrv +68: +68: Test +68: +68: BMS-986142_atrop8.mrv +68: +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: Test +68: +68: BMS-986142_atropBad2.mrv +68: +68: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +71: Randomness seeded to: 2014129356 +71: =============================================================================== +71: All tests passed (15 assertions in 3 test cases) +71: + 60/236 Test #71: testSquiggleDoubleBonds ................ Passed 0.04 sec +test 72 + Start 72: testMolSupplier + +72: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +72: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +72: Test timeout computed to be: 1500 +68: Test +68: +68: JDQ443_3d.mrv +68: +68: Test +68: +68: JDQ443_atrop1.mrv +68: +68: Test +68: +68: JDQ443_atrop2.mrv +68: +68: Test +68: +68: JDQ443_atrop3.mrv +68: +68: Test +68: +68: JDQ443_atropBad1.mrv +68: +68: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +68: Test +68: +68: RP-6306_atrop1.mrv +68: +68: Test +68: +68: RP-6306_atrop2.mrv +68: +68: Test +68: +68: RP-6306_atrop3.mrv +68: +68: Test +68: +68: RP-6306_atrop4.mrv +68: +68: Test +68: +68: RP-6306_atrop5.mrv +68: +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: Test +68: +68: RP-6306_atropBad1.mrv +68: +68: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +72: [23:38:04] +72: ----------------------------------------- +68: Test +68: +68: RP-6306_atropBad2.mrv +68: +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 + 61/236 Test #65: testDepictor ........................... Passed 0.74 sec +test 73 + Start 73: testGeneralFileReader + +73: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +73: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +73: Test timeout computed to be: 1500 +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: Atropisomers- 1 hits 3 misses +70: Final results: +70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses +72: [23:38:04] Ignoring invalid chirality label: '2_bad_chirality' +68: Test +68: +68: RP-6306_3d.mrv +68: +68: Test +68: +68: Sotorasib_atrop1.mrv +68: +68: Test +68: +68: Sotorasib_atrop2.mrv +68: +68: Test +68: +68: Sotorasib_atrop3.mrv +68: +68: Test +68: +68: Sotorasib_atrop4.mrv +68: +68: Test +68: +68: Sotorasib_atrop5.mrv +68: +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [23:38:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: Test +68: +68: Sotorasib_atropBad1.mrv +68: +68: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 + 62/236 Test #70: testAtropisomers ....................... Passed 0.30 sec +test 74 + Start 74: testMultithreadedMolSupplier + +74: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier +74: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +74: Test timeout computed to be: 1500 +68: Test +68: +68: Sotorasib_atropBad2.mrv +68: +68: [23:38:04] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +73: [23:38:04] +73: ----------------------------------------- +73: [23:38:04] Finished: testDetermineFormat() +73: [23:38:04] ----------------------------------------- +73: +73: [23:38:04] +73: ----------------------------------------- +68: Test +68: +68: Sotorasib_3d.mrv +68: +68: Test +68: +68: ZM374979_atrop1.mrv +68: +68: Test +68: +68: ZM374979_atrop2.mrv +68: +68: Test +68: +68: ZM374979_atrop3.mrv +68: +68: Test +68: +68: ZM374979_atropBad1.mrv +68: +68: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +74: [23:38:04] +74: ----------------------------------------- +68: Test +68: +68: mrtx1719_3d.mrv +68: +68: Test +68: +68: mrtx1719_atrop1.mrv +68: +68: Test +68: +68: mrtx1719_atrop2.mrv +68: +68: Test +68: +68: mrtx1719_atrop3.mrv +68: +68: Test +68: +68: mrtx1719_atropBad1.mrv +68: +68: [23:38:04] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +72: [23:38:04] Finished: testMolSup() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testRandMolSup() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +73: [23:38:04] Finished: testSdf() +73: [23:38:04] ----------------------------------------- +73: +73: [23:38:04] +73: ----------------------------------------- +68: Test +68: +68: AlexRxn.mrv +68: +68: Test +68: +68: BadReactionSign.mrv +68: +68: Test +68: +68: bondArray_node.mrv +68: +68: Test +68: +68: marvin03.mrv +68: +68: Test +68: +68: marvin04.mrv +68: +68: Test +68: +68: marvin08.mrv +68: +68: Test +68: +68: marvin09.mrv +68: +68: Test +68: +68: marvin11.mrv +68: +68: Test +68: +68: marvin05.mrv +68: +68: Test +68: +68: EmptyRxn.mrv +68: +68: [23:38:04] initialization failed +72: [23:38:04] Finished: testSmilesSup() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] ------------------------------------------------------ +72: [23:38:04] SMILES Parse Error: syntax error while parsing: fail +72: [23:38:04] SMILES Parse Error: check for mistakes around position 1: +72: [23:38:04] fail +72: [23:38:04] ^ +72: [23:38:04] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +72: [23:38:04] ERROR: Smiles parse error on line 3 +72: [23:38:04] ERROR: Cannot create molecule from : 'fail' +72: [23:38:04] ------------------------------------------------------ +72: [23:38:04] ------------------------------------------------------ +72: [23:38:04] >>> This may result in an infinite loop. It should finish almost immediately: +72: [23:38:04] <<< done. +72: [23:38:04] Finished: testSmilesSupFromText() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testSmilesWriter() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +67: ..............[23:38:04] SMILES Parse Error: syntax error while parsing: invalidsmiles +67: [23:38:04] SMILES Parse Error: check for mistakes around position 1: +67: [23:38:04] invalidsmiles +67: [23:38:04] ^ +67: [23:38:04] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' +72: [23:38:04] Finished: testSDWriter() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testSDSupplierEnding() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testSuppliersEmptyFile() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testCisTrans() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testStereoRound() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [23:38:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [23:38:04] Finished: testIssue226() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +73: [23:38:04] Finished: testSmi() +73: [23:38:04] ----------------------------------------- +73: +73: [23:38:04] +73: ----------------------------------------- +72: [23:38:04] Finished: testTDTSupplier1() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testTDTSupplier2() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testTDTSupplier3() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testSDSupplierFromText() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] ERROR: Problems encountered parsing data fields +72: [23:38:04] ERROR: moving to the beginning of the next molecule +72: [23:38:04] ERROR: Problems encountered parsing data fields +72: [23:38:04] ERROR: moving to the beginning of the next molecule +72: [23:38:04] Spurious data before the first property will be ignored +72: [23:38:04] Property will be truncated after the first blank line +72: [23:38:04] Property will be truncated after the first blank line +72: [23:38:04] Property will be truncated after the first blank line +72: [23:38:04] Finished: testSDSupplierStrLax1() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] ERROR: Problems encountered parsing data fields +72: [23:38:04] ERROR: moving to the beginning of the next molecule +72: [23:38:04] Property will be truncated after the first blank line +72: [23:38:04] Finished: testSDSupplierStrLax2() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] ERROR: Problems encountered parsing data fields +72: [23:38:04] ERROR: moving to the beginning of the next molecule +72: [23:38:04] ERROR: Problems encountered parsing data fields +72: [23:38:04] ERROR: moving to the beginning of the next molecule +72: [23:38:04] Spurious data before the first property will be ignored +72: [23:38:04] Property will be truncated after the first blank line +72: [23:38:04] Property will be truncated after the first blank line +72: [23:38:04] Property will be truncated after the first blank line +72: [23:38:04] Finished: testSDSupplierFromTextStrLax1() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] ERROR: Problems encountered parsing data fields +72: [23:38:04] ERROR: moving to the beginning of the next molecule +72: [23:38:04] Property will be truncated after the first blank line +72: [23:38:04] Finished: testSDSupplierFromTextStrLax2() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testIssue265() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] ERROR: End of data field name not found +72: [23:38:04] ERROR: moving to the beginning of the next molecule +72: [23:38:04] Explicit valence for atom # 0 F, 2, is greater than permitted +72: [23:38:04] ERROR: Could not sanitize molecule ending on line 16 +72: [23:38:04] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +72: [23:38:04] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +72: [23:38:04] ERROR: moving to the beginning of the next molecule +72: [23:38:04] ERROR: Bond line too short: 'M END' on line 18 +72: [23:38:04] ERROR: moving to the beginning of the next molecule +72: [23:38:04] Finished: testSDErrorHandling() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +68: Test +68: +68: RxnNoCoords.mrv +68: +68: Test +68: +68: mrvValenceZero.mrv +68: +68: Test +68: +68: condition_coordinates_mpoint.mrv +68: +68: Test +68: +68: marvin01.mrv +68: +68: Test +68: +68: aspirineSynthesisWithAttributes.mrv +68: +68: Test +68: +68: marvin01.mrv +68: +68: Test +68: +68: NewChiralTest +68: +68: Test +68: +68: NewChiralTest +68: +68: Test +68: +68: NewChiralTestNoChiral +68: +68: Test +68: +68: NewChiralTestNoChiral +68: +68: Test +68: +68: NewChiralTest2 +68: +68: Test +68: +68: NewChiralTest2 +68: +68: Test +68: +68: NewChiralTest2AllChiral +68: +68: Test +68: +68: NewChiralTest2AllChiral +68: +68: Test +68: +68: Vendor839 +68: +68: Test +68: +68: DoubleBondChain +68: +68: Test +68: +68: Na_Mg_Al_OH +68: +68: Test +68: +68: Pb +68: +68: Test +68: +68: O_Mg_Si +68: +68: Test +68: +68: SquiggleBond +68: +68: Test +68: +68: BigMacrocycle +68: +68: Test +68: +68: Smiles1 +68: +72: [23:38:04] Finished: testIssue381() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- + 63/236 Test #68: testMrvToMol ........................... Passed 0.74 sec +test 75 + Start 75: testMolWriter + +75: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter +75: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +75: Test timeout computed to be: 1500 +72: [23:38:04] Finished: testSetStreamIndices() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testMixIterAndRandom() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: build: +72: [23:38:04] Finished: testRemoveHs() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testGetItemText() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testForwardSDSupplier() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testMissingCRSDSupplier() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testIssue3482695() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] ERROR: Cannot convert 'foo' to unsigned int on line 557 +72: [23:38:04] ERROR: moving to the beginning of the next molecule +72: [23:38:04] Finished: testIssue3525673() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testBlankLinesInProps() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testSkipLines() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testGitHub23() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testGitHub88() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testGitHub2285() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +72: [23:38:04] ERROR: Smiles parse error on line 1 +72: [23:38:04] ERROR: Cannot create molecule from : 'c1ccccc' +72: [23:38:04] SMILES Parse Error: extra open parentheses while parsing: C(C +72: [23:38:04] SMILES Parse Error: check for mistakes around position 2: +72: [23:38:04] C(C +72: [23:38:04] ~^ +72: [23:38:04] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +72: [23:38:04] ERROR: Smiles parse error on line 3 +72: [23:38:04] ERROR: Cannot create molecule from : 'C(C' +72: [23:38:04] Explicit valence for atom # 1 C, 5, is greater than permitted +72: [23:38:04] ERROR: Could not sanitize molecule on line 5 +72: [23:38:04] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +72: [23:38:04] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [23:38:04] ERROR: Could not sanitize molecule ending on line 21 +72: [23:38:04] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [23:38:04] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [23:38:04] ERROR: Could not sanitize molecule ending on line 21 +72: [23:38:04] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [23:38:04] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [23:38:04] ERROR: Could not sanitize molecule ending on line 21 +72: [23:38:04] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [23:38:04] ERROR: Atom line too short: ' -9.6' on line 28 +72: [23:38:04] ERROR: moving to the beginning of the next molecule +72: [23:38:04] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [23:38:04] ERROR: Could not sanitize molecule ending on line 21 +72: [23:38:04] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [23:38:04] ERROR: Atom line too short: ' -9.6' on line 28 +72: [23:38:04] ERROR: moving to the beginning of the next molecule +72: [23:38:04] Finished: testGitHub2479() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Ignoring invalid chirality label: '7_S_8_9_6_10' +72: [23:38:04] Finished: testGitHub2881() +72: [23:38:04] ----------------------------------------- +72: +72: [23:38:04] ----------------------------------------- +72: [23:38:04] Finished: testGitHub3517() +72: [23:38:04] ----------------------------------------- +72: + 64/236 Test #72: testMolSupplier ........................ Passed 0.20 sec +test 76 + Start 76: testTplParser + +76: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testTplParser +76: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +76: Test timeout computed to be: 1500 + 65/236 Test #76: testTplParser .......................... Passed 0.02 sec +test 77 + Start 77: testMol2ToMol + +77: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol +77: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +77: Test timeout computed to be: 1500 +73: [23:38:05] Finished: testMae() +73: [23:38:05] ----------------------------------------- +73: +73: [23:38:05] +73: ----------------------------------------- +73: [23:38:05] Finished: testTdt() +73: [23:38:05] ----------------------------------------- +73: + 66/236 Test #73: testGeneralFileReader .................. Passed 0.18 sec test 78 Start 78: testSequence 78: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSequence 78: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 78: Test timeout computed to be: 1500 -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [03:09:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +67: ..... +67: ---------------------------------------------------------------------- +67: Ran 19 tests in 0.312s +67: +67: OK + 67/236 Test #77: testMol2ToMol .......................... Passed 0.03 sec +test 79 + Start 79: testExtendedStereoParsing + +79: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing +79: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +79: Test timeout computed to be: 1500 78: Sequence: GREG 78: HELM: PEPTIDE1{G.R.E.G}$$$$ 78: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O @@ -20526,137 +20979,51 @@ 78: CONECT 27 28 28 29 78: END 78: -68: Test -68: -68: RP-6306_3d.mrv -68: -68: Test -68: -68: Sotorasib_atrop1.mrv -68: -68: Test -68: -68: Sotorasib_atrop2.mrv -68: -68: Test -68: -68: Sotorasib_atrop3.mrv -68: -68: Test -68: -68: Sotorasib_atrop4.mrv -68: -68: Test -68: -68: Sotorasib_atrop5.mrv -68: -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: Test -68: -68: Sotorasib_atropBad1.mrv -68: -68: [03:09:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -68: Test -68: -68: Sotorasib_atropBad2.mrv -68: -68: [03:09:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 - 67/236 Test #77: testMol2ToMol .......................... Passed 0.11 sec - 68/236 Test #78: testSequence ........................... Passed 0.09 sec -test 79 - Start 79: testExtendedStereoParsing - -79: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing -79: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -79: Test timeout computed to be: 1500 + 68/236 Test #78: testSequence ........................... Passed 0.06 sec test 80 Start 80: fileParsersCatchTest 80: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 80: Test timeout computed to be: 1500 -69: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:09:36] deprecated group abbreviation ignored on line 24 -69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -69: [03:09:36] -69: -69: **** -69: Post-condition Violation -69: Element 'Mv' not found -69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -69: Failed Expression: anum > -1 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 3# 0x0000FFFF87DD7F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x0000FFFF87DE5B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x0000FFFF87DE6A4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 9# 0x0000AAAAB479F77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x0000AAAAB4814944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x0000AAAAB4785BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x0000FFFF874A229C in /lib/aarch64-linux-gnu/libc.so.6 -69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 14# 0x0000AAAAB4785E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -68: Test -68: -68: Sotorasib_3d.mrv -68: -68: Test -68: -68: ZM374979_atrop1.mrv -68: -68: Test -68: -68: ZM374979_atrop2.mrv -68: -68: Test -68: -68: ZM374979_atrop3.mrv -68: -68: Test -68: -68: ZM374979_atropBad1.mrv -68: -68: [03:09:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 - 69/236 Test #79: testExtendedStereoParsing .............. Passed 0.08 sec + 69/236 Test #79: testExtendedStereoParsing .............. Passed 0.06 sec test 81 Start 81: testPropertyLists 81: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists 81: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 81: Test timeout computed to be: 1500 -80: Randomness seeded to: 2162413122 -80: [03:09:36] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -80: [03:09:36] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [03:09:36] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [03:09:36] SGroup 1 is invalid and will be ignored -80: [03:09:36] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [03:09:36] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [03:09:36] SGroup 1 is invalid and will be ignored -80: [03:09:36] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -80: [03:09:36] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [03:09:36] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [03:09:36] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -80: [03:09:36] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [03:09:36] SGroup 1 is invalid and will be ignored -80: [03:09:36] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [03:09:36] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [03:09:36] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [03:09:36] SGroup 1 is invalid and will be ignored -80: [03:09:36] SGroup 3 referenced on line 40 not found. -80: [03:09:36] +81: Randomness seeded to: 3035453750 +81: =============================================================================== +81: All tests passed (95 assertions in 4 test cases) +81: + 70/236 Test #81: testPropertyLists ...................... Passed 0.05 sec +test 82 + Start 82: XYZFileParserCatchTest + +82: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest +82: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +82: Test timeout computed to be: 1500 +80: Randomness seeded to: 437369912 +80: [23:38:05] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +80: [23:38:05] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [23:38:05] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [23:38:05] SGroup 1 is invalid and will be ignored +80: [23:38:05] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [23:38:05] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [23:38:05] SGroup 1 is invalid and will be ignored +80: [23:38:05] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +80: [23:38:05] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [23:38:05] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [23:38:05] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +80: [23:38:05] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [23:38:05] SGroup 1 is invalid and will be ignored +80: [23:38:05] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [23:38:05] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [23:38:05] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [23:38:05] SGroup 1 is invalid and will be ignored +80: [23:38:05] SGroup 3 referenced on line 40 not found. +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -20669,24 +21036,24 @@ 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFF8E37EDE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFB89AEDE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# 0x0000AAAAC28E9C7C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 7# 0x0000AAAAB7CA9C7C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 16# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] SGroup 3 referenced on line 40 not found. -80: [03:09:36] +80: [23:38:05] SGroup 3 referenced on line 40 not found. +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -20699,29 +21066,29 @@ 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFF8E37EDE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFB89AEDE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# 0x0000AAAAC28E9CFC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 7# 0x0000AAAAB7CA9CFC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 16# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] no bonds -80: [03:09:36] SGroup 1 is invalid and will be ignored -80: [03:09:36] SGroup line too short: 'M SBV 1 6' on line 42 -80: [03:09:36] SGroup 1 is invalid and will be ignored -80: [03:09:36] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -80: [03:09:36] SGroup 2 is invalid and will be ignored -80: [03:09:36] +80: [23:38:05] no bonds +80: [23:38:05] SGroup 1 is invalid and will be ignored +80: [23:38:05] SGroup line too short: 'M SBV 1 6' on line 42 +80: [23:38:05] SGroup 1 is invalid and will be ignored +80: [23:38:05] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +80: [23:38:05] SGroup 2 is invalid and will be ignored +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -20735,23 +21102,23 @@ 80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFF8E37ED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB89AED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000AAAAC28EA6A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAB7CAA6A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -20765,24 +21132,24 @@ 80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFF8E37ED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB89AED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000AAAAC28EA724 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAB7CAA724 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] bookmark not found -80: [03:09:36] +80: [23:38:05] bookmark not found +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -20796,25 +21163,25 @@ 80: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFF8E37EDE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB89AEDE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000AAAAC28EA724 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAB7CAA724 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] bond is not part of the SubstanceGroup -80: [03:09:36] SGroup 2 is invalid and will be ignored -80: [03:09:36] +80: [23:38:05] bond is not part of the SubstanceGroup +80: [23:38:05] SGroup 2 is invalid and will be ignored +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -20828,23 +21195,23 @@ 80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFF8E37ED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB89AED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000AAAAC28EAA14 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAB7CAAA14 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -20858,27 +21225,27 @@ 80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFF8E37ED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB89AED50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000AAAAC28EAA94 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 8# 0x0000AAAAB7CAAA94 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 17# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 17# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] bookmark not found -80: [03:09:36] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -80: [03:09:36] SGroup 2 is invalid and will be ignored -80: [03:09:36] WARNING: final character of V3000 array is not ')' -80: [03:09:36] +80: [23:38:05] bookmark not found +80: [23:38:05] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +80: [23:38:05] SGroup 2 is invalid and will be ignored +80: [23:38:05] WARNING: final character of V3000 array is not ')' +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -20896,21 +21263,21 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAC28E8698 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB7CA8698 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] WARNING: final character of V3000 array is not ')' -80: [03:09:36] +80: [23:38:05] WARNING: final character of V3000 array is not ')' +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -20928,23 +21295,23 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAC28E8714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB7CA8714 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] bookmark not found -80: [03:09:36] SGroup 1 is invalid and will be ignored -80: [03:09:36] WARNING: final character of V3000 array is not ')' -80: [03:09:36] +80: [23:38:05] bookmark not found +80: [23:38:05] SGroup 1 is invalid and will be ignored +80: [23:38:05] WARNING: final character of V3000 array is not ')' +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -20962,21 +21329,21 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAC28E89E8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB7CA89E8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] WARNING: final character of V3000 array is not ')' -80: [03:09:36] +80: [23:38:05] WARNING: final character of V3000 array is not ')' +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -20994,22 +21361,22 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAC28E8A64 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB7CA8A64 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] bookmark not found -80: [03:09:36] SGroup 1 is invalid and will be ignored -80: [03:09:36] +80: [23:38:05] bookmark not found +80: [23:38:05] SGroup 1 is invalid and will be ignored +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -21027,20 +21394,20 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAC28E8D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB7CA8D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -21058,22 +21425,22 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAC28E8DB4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB7CA8DB4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] bookmark not found -80: [03:09:36] SGroup 2 is invalid and will be ignored -80: [03:09:36] +80: [23:38:05] bookmark not found +80: [23:38:05] SGroup 2 is invalid and will be ignored +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -21091,20 +21458,20 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAC28E9088 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB7CA9088 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -21122,62 +21489,48 @@ 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAC28E9104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB7CA9104 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] bookmark not found -80: [03:09:36] SGroup 2 is invalid and will be ignored -68: Test -68: -68: mrtx1719_3d.mrv -68: -68: Test -68: -68: mrtx1719_atrop1.mrv -68: -68: Test -68: -68: mrtx1719_atrop2.mrv -68: -68: Test -68: -68: mrtx1719_atrop3.mrv -68: -68: Test -68: -68: mrtx1719_atropBad1.mrv -68: -68: [03:09:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -80: [03:09:36] Explicit valence for atom # 2 O, 3, is greater than permitted -80: [03:09:36] Explicit valence for atom # 1 O, 3, is greater than permitted -80: [03:09:36] Explicit valence for atom # 1 C, 5, is greater than permitted -80: [03:09:36] sanitize [03:09:36] UNK: [03:09:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [03:09:36] skipping block at line 7: 'BEGIN ATOM' -81: Randomness seeded to: 3064755721 -81: =============================================================================== -81: All tests passed (95 assertions in 4 test cases) -81: - 70/236 Test #81: testPropertyLists ...................... Passed 0.06 sec -test 82 - Start 82: XYZFileParserCatchTest +80: [23:38:05] bookmark not found +80: [23:38:05] SGroup 2 is invalid and will be ignored +82: Randomness seeded to: 1978975744 +82: =============================================================================== +82: All tests passed (100 assertions in 2 test cases) +82: + 71/236 Test #82: XYZFileParserCatchTest ................. Passed 0.04 sec +test 83 + Start 83: cdxmlParserCatchTest -82: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest -82: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -82: Test timeout computed to be: 1500 +83: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest +83: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +83: Test timeout computed to be: 1500 +80: [23:38:05] Explicit valence for atom # 2 O, 3, is greater than permitted +80: [23:38:05] Explicit valence for atom # 1 O, 3, is greater than permitted +80: [23:38:05] Explicit valence for atom # 1 C, 5, is greater than permitted +80: [23:38:05] sanitize [23:38:05] UNK: [23:38:05] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. + 72/236 Test #67: pyDepictor ............................. Passed 1.09 sec +test 84 + Start 84: molfileStereoCatchTest + +84: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest +84: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +84: Test timeout computed to be: 1500 +80: [23:38:05] skipping block at line 7: 'BEGIN ATOM' 80: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL 80: END 80: -80: [03:09:36] +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -21189,21 +21542,21 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000AAAAC291DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAC28DB084 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAB7CDDBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAB7C9B084 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -21215,21 +21568,21 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000AAAAC291DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAC28DB1F4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAB7CDDBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAB7C9B1F4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -21241,21 +21594,21 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000AAAAC291DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAC28DB528 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAB7CDDBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAB7C9B528 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -21267,21 +21620,21 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000AAAAC291DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAC28DB7C4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAB7CDDBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAB7C9B7C4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -21293,29 +21646,29 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000AAAAC291DBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000AAAAC28DB9BC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 3# 0x0000AAAAB7CDDBC0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x0000AAAAB7C9B9BC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] Found a SCD/SED line with missing/empty SDT specification at line 21 -80: [03:09:36] Found a SCD/SED line with missing/empty SDT specification at line 20 -80: [03:09:36] BEGIN SGROUP line not found on line 14 -80: [03:09:36] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -80: [03:09:36] END SGROUP line not found on line 14 -80: [03:09:36] END SGROUP line not found on line 14 -80: [03:09:36] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -80: [03:09:36] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -80: [03:09:36] +80: [23:38:05] Found a SCD/SED line with missing/empty SDT specification at line 21 +80: [23:38:05] Found a SCD/SED line with missing/empty SDT specification at line 20 +80: [23:38:05] BEGIN SGROUP line not found on line 14 +80: [23:38:05] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +80: [23:38:05] END SGROUP line not found on line 14 +80: [23:38:05] END SGROUP line not found on line 14 +80: [23:38:05] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +80: [23:38:05] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +80: [23:38:05] 80: 80: **** 80: Range Error @@ -21330,38 +21683,43 @@ 80: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# 0x0000AAAAC291D834 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAC28E0A10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 6# 0x0000AAAAB7CDD834 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAB7CA0A10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 16# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -80: [03:09:36] Multiple ATTCHPT values for atom 2 on line 9 -80: [03:09:36] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [03:09:36] SMARTS Parse Error: syntax error while parsing: [#6;R -80: [03:09:36] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -80: [03:09:36] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -80: [03:09:36] Skipping empty SMARTS value for SMARTSQ. -80: [03:09:36] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -80: [03:09:36] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [03:09:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -80: [03:09:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [03:09:36] WARNING: Skipping property bar because the value includes an illegal blank line -80: [03:09:36] WARNING: Skipping property baz because the value includes an illegal blank line -80: [03:09:36] WARNING: Skipping property bletch +80: [23:38:05] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +80: [23:38:05] Multiple ATTCHPT values for atom 2 on line 9 +80: [23:38:05] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [23:38:05] SMARTS Parse Error: syntax error while parsing: [#6;R +80: [23:38:05] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +80: [23:38:05] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +80: [23:38:05] Skipping empty SMARTS value for SMARTSQ. +80: [23:38:05] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +80: [23:38:05] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [23:38:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +83: Randomness seeded to: 3244972242 +83: [23:38:05] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [23:38:05] Explicit valence for atom # 3 N, 4, is greater than permitted +83: [23:38:05] CDXMLParser: failed sanitizing skipping fragment 32 +83: [23:38:05] Bad bond in CDXML skipping fragment 58... +80: [23:38:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [23:38:05] WARNING: Skipping property bar because the value includes an illegal blank line +80: [23:38:05] WARNING: Skipping property baz because the value includes an illegal blank line +80: [23:38:05] WARNING: Skipping property bletch 80: nope because the name includes a newline -80: [03:09:36] WARNING: Skipping property bletch +80: [23:38:05] WARNING: Skipping property bletch 80: nope2 because the name includes a newline -80: [03:09:36] +80: [23:38:05] 80: 80: **** 80: Post-condition Violation @@ -21373,28 +21731,30 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000FFFF8E367F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFF8E378190 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFF8E378DCC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFFB8997F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFB89A8190 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB89A8DCC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAC28B4EF4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB7C74EF4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] +80: [23:38:05] 80: 80: **** +83: [23:38:05] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [23:38:05] Bad bond in CDXML skipping fragment 58... 80: Post-condition Violation 80: Element 'QQQ' not found 80: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h @@ -21404,26 +21764,26 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000FFFF8E367F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFF8E378190 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFF8E378DCC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFFB8997F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFB89A8190 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB89A8DCC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAC28B4818 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB7C74818 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] +80: [23:38:05] 80: 80: **** 80: Post-condition Violation @@ -21435,26 +21795,26 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000FFFF8E367F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFF8E375B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFF8E376A4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFFB8997F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFB89A5B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB89A6A4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAC28B4EB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB7C74EB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] +80: [23:38:05] 80: 80: **** 80: Post-condition Violation @@ -21466,28 +21826,61 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000FFFF8E367F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000FFFF8E375B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x0000FFFF8E376A4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x0000FFFFB8997F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x0000FFFFB89A5B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x0000FFFFB89A6A4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000AAAAC28B4BE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 9# 0x0000AAAAB7C74BE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 18# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:09:36] atom 3 has a negative isotope value. line: 15 -80: [03:09:36] Ignoring invalid chirality label: '2_bad_chirality' -80: [03:09:36] +80: [23:38:05] atom 3 has a negative isotope value. line: 15 +69: [23:38:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [23:38:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [23:38:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [23:38:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [23:38:05] deprecated group abbreviation ignored on line 24 +69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +69: [23:38:05] +69: +69: **** +69: Post-condition Violation +69: Element 'Mv' not found +69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +69: Failed Expression: anum > -1 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 3# 0x0000FFFF95897F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x0000FFFF958A5B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x0000FFFF958A6A4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 9# 0x0000AAAAD372F77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x0000AAAAD37A4944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x0000AAAAD3715BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x0000FFFF94F6229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +69: 14# 0x0000AAAAD3715E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +80: [23:38:05] Ignoring invalid chirality label: '2_bad_chirality' +80: [23:38:05] 80: 80: **** 80: Pre-condition Violation @@ -21500,330 +21893,115 @@ 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000AAAAC28F2054 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000AAAAC295EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000AAAAC295F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000AAAAC295F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000AAAAC2933D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000AAAAC2934284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000AAAAC28AC1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000FFFF8DA4229C in /lib/aarch64-linux-gnu/libc.so.6 +80: 4# 0x0000AAAAB7CB2054 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x0000AAAAB7D1EAAC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x0000AAAAB7D1F460 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x0000AAAAB7D1F894 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x0000AAAAB7CF3D38 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x0000AAAAB7CF4284 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x0000AAAAB7C6C1B0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x0000FFFFB807229C in /lib/aarch64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -80: 13# 0x0000AAAAC28AC270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x0000AAAAB7C6C270 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -82: Randomness seeded to: 2468330273 -82: =============================================================================== -82: All tests passed (100 assertions in 2 test cases) -82: - 71/236 Test #82: XYZFileParserCatchTest ................. Passed 0.04 sec -test 83 - Start 83: cdxmlParserCatchTest - -83: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest -83: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -83: Test timeout computed to be: 1500 -68: Test -68: -68: FalseAtropisomer.mrv -68: -68: Test -68: -68: AtropEnhancedStereo.mrv -68: -68: Test -68: -68: AtropManyChirals.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced2.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced3.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced4.mrv -68: -68: Test -68: -68: BMS-986142_3d_chiral.mrv -68: -68: Test -68: -68: BMS-986142_3d.mrv -68: -68: Test -68: -68: BMS-986142_atrop1.mrv -68: -68: Test -68: -68: BMS-986142_atrop2.mrv -68: -68: Test -68: -68: BMS-986142_atrop3.mrv -68: -68: Test -68: -68: BMS-986142_atrop4.mrv -68: -68: Test -68: -68: BMS-986142_atrop5.mrv -68: -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -29: All 191 tests passed -80: [03:09:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -68: Test -68: -68: BMS-986142_atrop6.mrv -68: -68: Test -68: -68: BMS-986142_atrop7.mrv -68: -68: Test -68: -68: BMS-986142_atrop8.mrv -68: -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: Test -68: -68: BMS-986142_atropBad2.mrv -68: -68: [03:09:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -80: [03:09:36] 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.[03:09:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [03:09:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [03:09:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [03:09:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -83: Randomness seeded to: 4050456081 -83: [03:09:36] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [03:09:36] Explicit valence for atom # 3 N, 4, is greater than permitted -83: [03:09:36] CDXMLParser: failed sanitizing skipping fragment 32 -83: [03:09:36] Bad bond in CDXML skipping fragment 58... -83: [03:09:36] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [03:09:36] Bad bond in CDXML skipping fragment 58... -68: Test -68: -68: JDQ443_3d.mrv -68: -68: Test -68: -68: JDQ443_atrop1.mrv -68: -68: Test -68: -68: JDQ443_atrop2.mrv -68: -68: Test -68: -68: JDQ443_atrop3.mrv -68: -68: Test -68: -68: JDQ443_atropBad1.mrv -68: -68: [03:09:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -83: [03:09:36] WARNING: not removing hydrogen atom without neighbors -83: [03:09:36] WARNING: not removing hydrogen atom without neighbors -83: [03:09:36] WARNING: not removing hydrogen atom without neighbors -83: [03:09:36] WARNING: not removing hydrogen atom without neighbors -83: [03:09:36] WARNING: not removing hydrogen atom without neighbors -83: [03:09:36] WARNING: not removing hydrogen atom without neighbors -83: [03:09:36] WARNING: not removing hydrogen atom without neighbors -83: [03:09:36] WARNING: not removing hydrogen atom without neighbors -83: [03:09:36] WARNING: not removing hydrogen atom without neighbors -83: [03:09:36] WARNING: not removing hydrogen atom without neighbors -83: [03:09:36] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. -68: Test -68: -68: RP-6306_atrop1.mrv -68: -68: Test -68: -68: RP-6306_atrop2.mrv -68: -68: Test -68: -68: RP-6306_atrop3.mrv -68: -68: Test -68: -68: RP-6306_atrop4.mrv -68: -68: Test -68: -68: RP-6306_atrop5.mrv -68: -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: Test -68: -68: RP-6306_atropBad1.mrv -68: -68: [03:09:36] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -68: Test -68: -68: RP-6306_atropBad2.mrv -68: -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [03:09:36] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -83: [03:09:36] Incomplete atom labelling, cannot make bond -83: [03:09:36] Incomplete atom labelling, cannot make bond -83: [03:09:36] Incomplete atom labelling, cannot make bond -69: [03:09:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -69: [03:09:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -68: Test -68: -68: RP-6306_3d.mrv -68: -68: Test -68: -68: Sotorasib_atrop1.mrv -68: -68: Test -68: -68: Sotorasib_atrop2.mrv -68: -68: Test -68: -68: Sotorasib_atrop3.mrv -68: -68: Test -68: -68: Sotorasib_atrop4.mrv -68: -68: Test -68: -68: Sotorasib_atrop5.mrv -68: -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [03:09:36] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -83: [03:09:36] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [03:09:36] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [03:09:36] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -83: [03:09:36] Failed to parse XML fragment 5 node: b attribute: Order: 5 -83: [03:09:36] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: =============================================================================== -83: All tests passed (263 assertions in 7 test cases) -83: - 72/236 Test #83: cdxmlParserCatchTest ................... Passed 0.19 sec -test 84 - Start 84: molfileStereoCatchTest - -84: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest -84: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -84: Test timeout computed to be: 1500 -68: Test -68: -68: Sotorasib_atropBad1.mrv -68: -68: [03:09:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -68: Test -68: -68: Sotorasib_atropBad2.mrv -68: -68: [03:09:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -84: Randomness seeded to: 958371747 -84: [03:09:37] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [03:09:37] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [03:09:37] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [03:09:37] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: Randomness seeded to: 260020416 +84: [23:38:05] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [23:38:05] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [23:38:05] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [23:38:05] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 84: =============================================================================== 84: All tests passed (142 assertions in 6 test cases) 84: - 73/236 Test #84: molfileStereoCatchTest ................. Passed 0.05 sec +83: [23:38:05] WARNING: not removing hydrogen atom without neighbors +83: [23:38:05] WARNING: not removing hydrogen atom without neighbors +83: [23:38:05] WARNING: not removing hydrogen atom without neighbors +83: [23:38:05] WARNING: not removing hydrogen atom without neighbors +83: [23:38:05] WARNING: not removing hydrogen atom without neighbors +83: [23:38:05] WARNING: not removing hydrogen atom without neighbors + 73/236 Test #84: molfileStereoCatchTest ................. Passed 0.08 sec test 85 Start 85: connectTheDotsTest 85: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest 85: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 85: Test timeout computed to be: 1500 -68: Test -68: -68: Sotorasib_3d.mrv -68: -68: Test -68: -68: ZM374979_atrop1.mrv -68: -68: Test -68: -68: ZM374979_atrop2.mrv -68: -68: Test -68: -68: ZM374979_atrop3.mrv -68: -68: Test -68: -68: ZM374979_atropBad1.mrv -68: -68: [03:09:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -68: Test -68: -68: mrtx1719_3d.mrv -68: -68: Test -68: -68: mrtx1719_atrop1.mrv -68: -68: Test -68: -68: mrtx1719_atrop2.mrv -68: -68: Test -68: -68: mrtx1719_atrop3.mrv -68: -68: Test -68: -68: mrtx1719_atropBad1.mrv -68: -68: [03:09:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -85: Randomness seeded to: 3129188826 +83: [23:38:05] WARNING: not removing hydrogen atom without neighbors +83: [23:38:05] WARNING: not removing hydrogen atom without neighbors +83: [23:38:05] WARNING: not removing hydrogen atom without neighbors +83: [23:38:05] WARNING: not removing hydrogen atom without neighbors +83: [23:38:05] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +83: [23:38:05] Incomplete atom labelling, cannot make bond +83: [23:38:05] Incomplete atom labelling, cannot make bond +75: [23:38:05] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +75: 0.40201265 0.40201265 +75: -0.13299436 -0.13299436 +75: 1.00000017 1.00000017 +75: 0.8762226 0.8762226 +75: 0.9973909 0.9973909 +75: 1.00000003 1.00000003 +75: 0.36613799 0.36613799 +75: 2.1107185 2.1107185 +75: 0.99999982 0.99999982 +75: 2.48696157 2.48696157 +75: 1.00479935 1.00479935 +75: 0.99999999 0.99999999 +75: 3.03311841 3.03311841 +75: 2.23739955 2.23739955 +75: 1.0000001 1.0000001 +75: 3.00772337 3.00772337 +75: 0.37399294 0.37399294 +75: 2.07713325 2.07713325 +75: 3.0077234 3.0077234 +75: 0.37399312 0.37399312 +75: -0.07713336 -0.07713336 +75: [23:38:05] bond with order 0 found on line 11. This is not part of the MDL specification. +75: [23:38:05] bond with order 0 found on line 16. This is not part of the MDL specification. +83: [23:38:05] Incomplete atom labelling, cannot make bond +69: [23:38:05] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: [23:38:05] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +85: Randomness seeded to: 3170285304 85: =============================================================================== 85: All tests passed (8 assertions in 1 test case) 85: - 74/236 Test #85: connectTheDotsTest ..................... Passed 0.05 sec + 74/236 Test #85: connectTheDotsTest ..................... Passed 0.07 sec test 86 Start 86: v2MolSuppliers 86: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers 86: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 86: Test timeout computed to be: 1500 -86: Randomness seeded to: 2158201800 -86: [03:09:37] Ignoring invalid chirality label: '12_R_1_3_4_5' -86: [03:09:37] Ignoring invalid chirality label: '12_ANR_1_3_4_15' -86: [03:09:37] Ignoring invalid chirality label: '2_S_1_3_4' -86: [03:09:37] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' -86: =============================================================================== -86: All tests passed (24 assertions in 6 test cases) -86: - 75/236 Test #86: v2MolSuppliers ......................... Passed 0.06 sec +83: [23:38:05] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [23:38:05] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [23:38:05] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +83: [23:38:05] Failed to parse XML fragment 5 node: b attribute: Order: 5 +83: [23:38:05] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: =============================================================================== +83: All tests passed (263 assertions in 7 test cases) +83: + 75/236 Test #75: testMolWriter .......................... Passed 0.43 sec test 87 Start 87: v2FileParsersCatchTest 87: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest 87: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 87: Test timeout computed to be: 1500 +80: [23:38:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +80: [23:38:05] 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.[23:38:05] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +80: [23:38:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [23:38:05] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +80: [23:38:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 76/236 Test #83: cdxmlParserCatchTest ................... Passed 0.21 sec +test 88 + Start 88: atropisomersCatch + +88: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/atropisomersCatch +88: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +88: Test timeout computed to be: 1500 69: ---------------------------------- 69: ---------------------------------- -69: [03:09:37] +69: [23:38:05] 69: 69: **** 69: Pre-condition Violation @@ -21835,168 +22013,32 @@ 69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -69: 3# 0x0000AAAAB47AF23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x0000AAAAB48149A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x0000AAAAB4785BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x0000FFFF874A229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 3# 0x0000AAAAD373F23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x0000AAAAD37A49A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x0000AAAAD3715BF8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x0000FFFF94F6229C in /lib/aarch64-linux-gnu/libc.so.6 69: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 8# 0x0000AAAAB4785E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 8# 0x0000AAAAD3715E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: ---------- 69: **** 69: -69: [03:09:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -68: Test -68: -68: AlexRxn.mrv -68: -68: Test -68: -68: BadReactionSign.mrv -68: -68: Test -68: -68: bondArray_node.mrv -68: -68: Test -68: -68: marvin03.mrv -68: -68: Test -68: -68: marvin04.mrv -68: -68: Test -68: -68: marvin08.mrv -68: -68: Test -68: -68: marvin09.mrv -68: -68: Test -68: -68: marvin11.mrv -68: -68: Test -68: -68: marvin05.mrv -68: -68: Test -68: -68: EmptyRxn.mrv -68: -68: [03:09:37] initialization failed -87: Randomness seeded to: 945930942 +69: [23:38:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +87: Randomness seeded to: 398592956 87: =============================================================================== 87: All tests passed (6 assertions in 1 test case) 87: - 76/236 Test #87: v2FileParsersCatchTest ................. Passed 0.04 sec -test 88 - Start 88: atropisomersCatch - -88: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/atropisomersCatch -88: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -88: Test timeout computed to be: 1500 -68: Test -68: -68: RxnNoCoords.mrv -68: -68: Test -68: -68: mrvValenceZero.mrv -68: -68: Test -68: -68: condition_coordinates_mpoint.mrv -68: -68: Test -68: -68: marvin01.mrv -68: -68: Test -68: -68: aspirineSynthesisWithAttributes.mrv -68: -68: Test -68: -68: marvin01.mrv -68: -68: Test -68: -68: NewChiralTest -68: -68: Test -68: -68: NewChiralTest -68: -68: Test -68: -68: NewChiralTestNoChiral -68: -68: Test -68: -68: NewChiralTestNoChiral -68: -68: Test -68: -68: NewChiralTest2 -68: -68: Test -68: -68: NewChiralTest2 -68: -68: Test -68: -68: NewChiralTest2AllChiral -68: -68: Test -68: -68: NewChiralTest2AllChiral -68: -68: Test -68: -68: Vendor839 -68: -68: Test -68: -68: DoubleBondChain -68: -68: Test -68: -68: Na_Mg_Al_OH -68: -68: Test -68: -68: Pb -68: -68: Test -68: -68: O_Mg_Si -68: -68: Test -68: -68: SquiggleBond -68: -68: Test -68: -68: BigMacrocycle -68: -68: Test -68: -68: Smiles1 -68: - 77/236 Test #68: testMrvToMol ........................... Passed 1.77 sec + 77/236 Test #87: v2FileParsersCatchTest ................. Passed 0.07 sec test 89 Start 89: multithreadedSupplierCatchTest 89: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest 89: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 89: Test timeout computed to be: 1500 -88: Randomness seeded to: 824498164 +88: Randomness seeded to: 1576268084 88: =============================================================================== 88: All tests passed (26 assertions in 2 test cases) 88: - 78/236 Test #88: atropisomersCatch ...................... Passed 0.05 sec + 78/236 Test #88: atropisomersCatch ...................... Passed 0.06 sec test 90 Start 90: testSubstructMatch @@ -22027,33 +22069,18 @@ 90: ----------------- Testing serial numbers on recursive queries 90: Done 90: -90: [03:09:37] ------------------------------------- -90: [03:09:37] Test multithreading +90: [23:38:05] ------------------------------------- +90: [23:38:05] Test multithreading 90: reading molecules -60: Test -60: -60: AtropCanon1.cxsmi -60: -60: Test -60: -60: AtropCanon2.cxsmi -60: -60: Test -60: -60: AtropCanon3.cxsmi -60: -60: Test -60: -60: BMS-986142_3d_chiral.cxsmi -60: -60: Test -60: -60: BMS-986142_3d.cxsmi -60: -60: =============================================================================== -60: All tests passed (2496 assertions in 31 test cases) -60: - 79/236 Test #60: cxsmilesTest ........................... Passed 2.17 sec +86: Randomness seeded to: 776545569 +86: [23:38:05] Ignoring invalid chirality label: '12_R_1_3_4_5' +86: [23:38:05] Ignoring invalid chirality label: '12_ANR_1_3_4_15' +86: [23:38:05] Ignoring invalid chirality label: '2_S_1_3_4' +86: [23:38:05] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' +86: =============================================================================== +86: All tests passed (24 assertions in 6 test cases) +86: + 79/236 Test #86: v2MolSuppliers ......................... Passed 0.15 sec test 91 Start 91: substructTestCatch @@ -22066,6 +22093,12 @@ 90: launch :1 90: launch :2 90: launch :3 +69: [23:38:05] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [23:38:05] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +69: [23:38:05] Empty atom list: 'M ALS 1 0 F' on line 8. +69: de_DE.UTF-8 +69: [23:38:05] ------------------------------------- +69: [23:38:05] Test multithreading Locale Switching 90: done 90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 90: processing2 @@ -22073,6 +22106,12 @@ 90: launch2 :1 90: launch2 :2 90: launch2 :3 +69: [23:38:05] Test multithreading (Done) +69: [23:38:05] ------------------------------------- +69: *************************************** +69: *************************************** +69: [23:38:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [23:38:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 90: done 90: preprocessing 3 90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 @@ -22081,35 +22120,43 @@ 90: launch3 :1 90: launch3 :2 90: launch3 :3 +69: [23:38:05] bond with order 0 found on line 7. This is not part of the MDL specification. +69: [23:38:05] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [23:38:05] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +69: [23:38:05] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: generating smiles +69: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 +69: converting back +69: check isomorphism 90: done -90: [03:09:37] done -90: [03:09:37] ------------------------------------- -90: [03:09:37] Test GitHub issue 15 -90: [03:09:37] done -90: [03:09:37] ------------------------------------- -90: [03:09:37] Test GitHub issue 409 -90: [03:09:37] done -90: [03:09:37] ------------------------------------- -90: [03:09:37] Test chiral matching -90: [03:09:37] done -90: [03:09:37] ------------------------------------- -90: [03:09:37] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -90: [03:09:37] done -90: [03:09:37] ------------------------------------- -90: [03:09:37] Test dative-bond matching -90: [03:09:37] done -90: [03:09:37] ------------------------------------- -90: [03:09:37] Test cis/trans matching -90: [03:09:37] done -90: [03:09:37] ------------------------------------- -90: [03:09:37] Test cis/trans matching part 2 -90: [03:09:37] done -90: [03:09:37] ------------------------------------- -90: [03:09:37] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -90: [03:09:37] done -90: [03:09:37] ------------------------------------- -90: [03:09:37] Testing matching E/Z against Cis/Trans stereo bonds -90: [03:09:37] +90: [23:38:05] done +90: [23:38:05] ------------------------------------- +90: [23:38:05] Test GitHub issue 15 +90: [23:38:05] done +90: [23:38:05] ------------------------------------- +90: [23:38:05] Test GitHub issue 409 +90: [23:38:05] done +90: [23:38:05] ------------------------------------- +90: [23:38:05] Test chiral matching +90: [23:38:05] done +90: [23:38:05] ------------------------------------- +90: [23:38:05] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +90: [23:38:05] done +90: [23:38:05] ------------------------------------- +90: [23:38:05] Test dative-bond matching +90: [23:38:05] done +90: [23:38:05] ------------------------------------- +90: [23:38:05] Test cis/trans matching +90: [23:38:05] done +90: [23:38:05] ------------------------------------- +90: [23:38:05] Test cis/trans matching part 2 +90: [23:38:05] done +90: [23:38:05] ------------------------------------- +90: [23:38:05] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +90: [23:38:05] done +90: [23:38:05] ------------------------------------- +90: [23:38:05] Testing matching E/Z against Cis/Trans stereo bonds +90: [23:38:05] 90: 90: **** 90: Pre-condition Violation @@ -22122,15 +22169,15 @@ 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x0000AAAAAD65AD50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000AAAAAD6499A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x0000FFFFA880229C in /lib/aarch64-linux-gnu/libc.so.6 +90: 4# 0x0000AAAAACD5AD50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x0000AAAAACD499A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x0000FFFF91FB229C in /lib/aarch64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -90: 8# 0x0000AAAAAD649BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 8# 0x0000AAAAACD49BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: -90: [03:09:37] +90: [23:38:05] 90: 90: **** 90: Pre-condition Violation @@ -22143,32 +22190,232 @@ 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 3# RDKit::sortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x0000AAAAAD65B3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000AAAAAD6499A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x0000FFFFA880229C in /lib/aarch64-linux-gnu/libc.so.6 +90: 4# 0x0000AAAAACD5B3A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x0000AAAAACD499A8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x0000FFFF91FB229C in /lib/aarch64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -90: 8# 0x0000AAAAAD649BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 8# 0x0000AAAAACD49BB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: -90: [03:09:37] ------------------------------------- -90: [03:09:37] Test substructure matching with a pathological case for symmetric SSSR -90: [03:09:37] ------------------------------------- -90: [03:09:37] Test isAtomTerminalRGroupOrQueryHydrogen - 80/236 Test #90: testSubstructMatch ..................... Passed 0.41 sec +90: [23:38:05] ------------------------------------- +90: [23:38:05] Test substructure matching with a pathological case for symmetric SSSR +90: [23:38:05] ------------------------------------- +90: [23:38:05] Test isAtomTerminalRGroupOrQueryHydrogen + 80/236 Test #90: testSubstructMatch ..................... Passed 0.35 sec test 92 Start 92: testGenericGroups 92: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups 92: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups 92: Test timeout computed to be: 1500 -91: Randomness seeded to: 3086873615 +89: Randomness seeded to: 4174527402 +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:05] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:06] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:06] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:06] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:06] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:06] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:06] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:06] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:06] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [23:38:06] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +91: Randomness seeded to: 3463455832 91: =============================================================================== 91: All tests passed (242 assertions in 12 test cases) 91: -69: [03:09:37] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [03:09:37] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' - 81/236 Test #91: substructTestCatch ..................... Passed 0.39 sec + 81/236 Test #91: substructTestCatch ..................... Passed 0.50 sec test 93 Start 93: testReaction @@ -22178,566 +22425,264 @@ 93: smi: O=C1CNC(=O)CN1 93: 1: O=C1CNC(=O)CN1 93: 2: COOC -93: [03:09:37] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [03:09:37] 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: [23:38:06] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [23:38:06] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 93: O=C1CNC(=O)CN1 -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] mapped atoms in the reactants were not mapped in the products. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [03:09:37] atom 0 in product 0 has multiple charge specifications. +93: [23:38:06] atom 0 in product 0 has multiple charge specifications. 93: mass: 15.0001 93: Oc1ccccn1 93: Oc1ccc[nH]1 -93: [03:09:37] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -93: [03:09:37] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -93: [03:09:37] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [03:09:37] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [03:09:37] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -93: [03:09:37] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -93: [03:09:37] SMARTS Parse Error: syntax error while parsing: [C:2]) -93: [03:09:37] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -93: [03:09:37] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [03:09:37] SMILES Parse Error: check for mistakes around position 2: -93: [03:09:37] [Q:1][C:2][C:3](=[O:4])[O:5] -93: [03:09:37] ~^ -93: [03:09:37] 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: [03:09:37] reactant 2 has no mapped atoms. -93: [03:09:37] >> Atoms within one molecule have different RXN roles. -93: [03:09:37] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -93: [03:09:37] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -93: [03:09:37] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -93: [03:09:37] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [03:09:37] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [03:09:37] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -93: [03:09:37] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -93: [03:09:37] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -93: [03:09:37] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -93: [03:09:37] reactant 0 has no mapped atoms. -93: [03:09:37] reactant 1 has no mapped atoms. -93: [03:09:37] reactant 3 has no mapped atoms. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 4 found multiple times. -93: [03:09:37] product atom-mapping number 5 found multiple times. -93: [03:09:37] product atom-mapping number 6 found multiple times. -93: [03:09:37] product atom-mapping number 7 found multiple times. -93: [03:09:37] product atom-mapping number 8 found multiple times. -93: [03:09:37] product atom-mapping number 12 found multiple times. -93: [03:09:37] product atom-mapping number 9 found multiple times. -93: [03:09:37] product atom-mapping number 10 found multiple times. -93: [03:09:37] product atom-mapping number 11 found multiple times. -93: [03:09:37] reactant 0 has no mapped atoms. -93: [03:09:37] reactant 1 has no mapped atoms. -93: [03:09:37] reactant 3 has no mapped atoms. -93: [03:09:37] reactant atom-mapping number 19 found multiple times. -93: [03:09:37] reactant atom-mapping number 25 found multiple times. -93: [03:09:37] reactant atom-mapping number 20 found multiple times. -93: [03:09:37] reactant atom-mapping number 21 found multiple times. -93: [03:09:37] reactant atom-mapping number 22 found multiple times. -93: [03:09:37] reactant atom-mapping number 23 found multiple times. -93: [03:09:37] reactant atom-mapping number 24 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. +93: [23:38:06] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +93: [23:38:06] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +93: [23:38:06] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [23:38:06] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [23:38:06] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +93: [23:38:06] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +93: [23:38:06] SMARTS Parse Error: syntax error while parsing: [C:2]) +93: [23:38:06] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +93: [23:38:06] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [23:38:06] SMILES Parse Error: check for mistakes around position 2: +93: [23:38:06] [Q:1][C:2][C:3](=[O:4])[O:5] +93: [23:38:06] ~^ +93: [23:38:06] 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: [23:38:06] reactant 2 has no mapped atoms. +93: [23:38:06] >> Atoms within one molecule have different RXN roles. +93: [23:38:06] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +93: [23:38:06] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +93: [23:38:06] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +93: [23:38:06] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [23:38:06] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [23:38:06] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +93: [23:38:06] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +93: [23:38:06] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +93: [23:38:06] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +93: [23:38:06] reactant 0 has no mapped atoms. +93: [23:38:06] reactant 1 has no mapped atoms. +93: [23:38:06] reactant 3 has no mapped atoms. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 4 found multiple times. +93: [23:38:06] product atom-mapping number 5 found multiple times. +93: [23:38:06] product atom-mapping number 6 found multiple times. +93: [23:38:06] product atom-mapping number 7 found multiple times. +93: [23:38:06] product atom-mapping number 8 found multiple times. +93: [23:38:06] product atom-mapping number 12 found multiple times. +93: [23:38:06] product atom-mapping number 9 found multiple times. +93: [23:38:06] product atom-mapping number 10 found multiple times. +93: [23:38:06] product atom-mapping number 11 found multiple times. +93: [23:38:06] reactant 0 has no mapped atoms. +93: [23:38:06] reactant 1 has no mapped atoms. +93: [23:38:06] reactant 3 has no mapped atoms. +93: [23:38:06] reactant atom-mapping number 19 found multiple times. +93: [23:38:06] reactant atom-mapping number 25 found multiple times. +93: [23:38:06] reactant atom-mapping number 20 found multiple times. +93: [23:38:06] reactant atom-mapping number 21 found multiple times. +93: [23:38:06] reactant atom-mapping number 22 found multiple times. +93: [23:38:06] reactant atom-mapping number 23 found multiple times. +93: [23:38:06] reactant atom-mapping number 24 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [03:09:37] product atom-mapping number 5 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 4 found multiple times. -93: [03:09:37] product atom-mapping number 5 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 4 found multiple times. +93: [23:38:06] product atom-mapping number 5 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 4 found multiple times. +93: [23:38:06] product atom-mapping number 5 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [03:09:37] product atom-mapping number 5 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 4 found multiple times. -93: [03:09:37] product atom-mapping number 5 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 4 found multiple times. +93: [23:38:06] product atom-mapping number 5 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 4 found multiple times. +93: [23:38:06] product atom-mapping number 5 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 4 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 4 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 4 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 4 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 4 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 4 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)O[C@](F)(Cl)Br -93: [03:09:37] product atom-mapping number 4 found multiple times. -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 4 found multiple times. -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 4 found multiple times. -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 4 found multiple times. -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] mapped atoms in the reactants were not mapped in the products. +93: [23:38:06] product atom-mapping number 4 found multiple times. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 4 found multiple times. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 4 found multiple times. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 4 found multiple times. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [03:09:37] product atom-mapping number 3 found multiple times. -93: [03:09:37] product atom-mapping number 2 found multiple times. -93: [03:09:37] product atom-mapping number 1 found multiple times. -93: [03:09:37] mapped atoms in the reactants were not mapped in the products. +93: [23:38:06] product atom-mapping number 3 found multiple times. +93: [23:38:06] product atom-mapping number 2 found multiple times. +93: [23:38:06] product atom-mapping number 1 found multiple times. +93: [23:38:06] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [03:09:37] product atom-mapping number 6 not found in reactants. -93: [03:09:37] product atom-mapping number 7 not found in reactants. -93: [03:09:37] product atom-mapping number 8 not found in reactants. -93: [03:09:37] product atom-mapping number 7 not found in reactants. -93: [03:09:37] product atom-mapping number 8 not found in reactants. -93: [03:09:37] product atom-mapping number 9 not found in reactants. -93: [03:09:37] product atom-mapping number 10 not found in reactants. -93: [03:09:37] mapped atoms in the reactants were not mapped in the products. +93: [23:38:06] product atom-mapping number 6 not found in reactants. +93: [23:38:06] product atom-mapping number 7 not found in reactants. +93: [23:38:06] product atom-mapping number 8 not found in reactants. +93: [23:38:06] product atom-mapping number 7 not found in reactants. +93: [23:38:06] product atom-mapping number 8 not found in reactants. +93: [23:38:06] product atom-mapping number 9 not found in reactants. +93: [23:38:06] product atom-mapping number 10 not found in reactants. +93: [23:38:06] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 -93: [03:09:37] product atom-mapping number 7 not found in reactants. -93: [03:09:37] product atom-mapping number 8 not found in reactants. -93: [03:09:37] product atom-mapping number 9 not found in reactants. -93: [03:09:37] product atom-mapping number 10 not found in reactants. -93: [03:09:37] mapped atoms in the reactants were not mapped in the products. +93: [23:38:06] product atom-mapping number 7 not found in reactants. +93: [23:38:06] product atom-mapping number 8 not found in reactants. +93: [23:38:06] product atom-mapping number 9 not found in reactants. +93: [23:38:06] product atom-mapping number 10 not found in reactants. +93: [23:38:06] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 -69: [03:09:37] Empty atom list: 'M ALS 1 0 F' on line 8. -69: de_DE.UTF-8 -69: [03:09:37] ------------------------------------- -69: [03:09:37] Test multithreading Locale Switching 93: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 93: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] -93: [03:09:37] mapped atoms in the reactants were not mapped in the products. +93: [23:38:06] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 -69: [03:09:37] Test multithreading (Done) -69: [03:09:37] ------------------------------------- -93: [03:09:37] product atom-mapping number 17 not found in reactants. -93: [03:09:37] product atom-mapping number 18 not found in reactants. -93: [03:09:37] mapped atoms in the reactants were not mapped in the products. +93: [23:38:06] product atom-mapping number 17 not found in reactants. +93: [23:38:06] product atom-mapping number 18 not found in reactants. +93: [23:38:06] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 12 -69: *************************************** -69: *************************************** -89: Randomness seeded to: 2821611777 -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -69: [03:09:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [03:09:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -69: [03:09:37] bond with order 0 found on line 7. This is not part of the MDL specification. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -69: [03:09:37] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [03:09:37] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [03:09:37] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -69: generating smiles -69: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -69: converting back -69: check isomorphism -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -93: [03:09:37] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: [03:09:37] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: -93: [03:09:37] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -93: ------------- -93: CCOc1ccccc1 -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:09:38] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -40: [03:09:38] done: 500000 -40: [03:09:38] Done -93: [03:09:38] reactant 0 has no mapped atoms. -93: [03:09:38] product 0 has no mapped atoms. -93: [03:09:38] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. - 82/236 Test #93: testReaction ........................... Passed 0.50 sec +92: Randomness seeded to: 2508404614 +92: =============================================================================== +92: All tests passed (11480 assertions in 38 test cases) +92: + 82/236 Test #92: testGenericGroups ...................... Passed 0.48 sec test 94 Start 94: testReactionFingerprints 94: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints 94: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 94: Test timeout computed to be: 1500 -40: [03:09:38] Testing hanoi with a functor. -40: [03:09:38] Done -40: [03:09:38] Testing basic partition refinement. -40: [03:09:38] Done -40: [03:09:38] Testing partition refinement with neighbors. -40: [03:09:38] Done -40: [03:09:38] testing canonicalization via tie breaking. -40: [03:09:38] Done -40: [03:09:38] testing canonicalization using the wrapper. -94: [03:09:38] ------------------------------------- -94: [03:09:38] Test Reaction StructuralFingerprint -40: [03:09:38] Done -40: [03:09:38] testing some specific ordering problems -40: [03:09:38] Finished -40: [03:09:38] testing chiral invariants. -40: [03:09:38] Finished -40: [03:09:38] testing unique ranks in w.r.t. renumbering. -94: [03:09:38] ------------------------------------- -94: [03:09:38] Test Reaction DifferenceFingerprint - 83/236 Test #94: testReactionFingerprints ............... Passed 0.06 sec +93: [23:38:06] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: [23:38:06] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: +93: [23:38:06] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +93: ------------- +93: CCOc1ccccc1 +94: [23:38:06] ------------------------------------- +94: [23:38:06] Test Reaction StructuralFingerprint +94: [23:38:06] ------------------------------------- +94: [23:38:06] Test Reaction DifferenceFingerprint + 83/236 Test #94: testReactionFingerprints ............... Passed 0.07 sec test 95 Start 95: testEnumeration 95: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration 95: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 95: Test timeout computed to be: 1500 -40: [03:09:38] Finished -40: [03:09:38] testing mol fragments. -40: [03:09:38] Finished -40: [03:09:38] testing protein round-tripping. +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +89: [23:38:06] Explicit valence for atom # 9 N, 5, is greater than permitted +89: [23:38:06] Explicit valence for atom # 3 Al, 6, is greater than permitted 95: 30000000 30000000 -92: Randomness seeded to: 1220223590 -92: =============================================================================== -92: All tests passed (11480 assertions in 38 test cases) -92: - 84/236 Test #92: testGenericGroups ...................... Passed 0.83 sec +89: [23:38:06] Explicit valence for atom # 4 Al, 6, is greater than permitted +29: All 191 tests passed +89: [23:38:06] Explicit valence for atom # 10 Si, 6, is greater than permitted +93: [23:38:06] reactant 0 has no mapped atoms. +93: [23:38:06] product 0 has no mapped atoms. +93: [23:38:06] 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 0.65 sec test 96 Start 96: rxnTestCatch 96: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch 96: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 96: Test timeout computed to be: 1500 -96: Randomness seeded to: 2282595257 -96: [03:09:38] atom 0 in product 0 has multiple charge specifications. -96: [03:09:38] Found a SCD/SED line with missing/empty SDT specification at line 34 -96: [03:09:38] Found a SCD/SED line with missing/empty SDT specification at line 36 -96: [03:09:38] Found a SCD/SED line with missing/empty SDT specification at line 38 -96: [03:09:38] Found a SCD/SED line with missing/empty SDT specification at line 40 -96: [03:09:38] Found a SCD/SED line with missing/empty SDT specification at line 42 -96: [03:09:38] Found a SCD/SED line with missing/empty SDT specification at line 87 -96: [03:09:38] Found a SCD/SED line with missing/empty SDT specification at line 89 -96: [03:09:38] Found a SCD/SED line with missing/empty SDT specification at line 91 -96: [03:09:38] Found a SCD/SED line with missing/empty SDT specification at line 93 -96: [03:09:38] Found a SCD/SED line with missing/empty SDT specification at line 95 -96: [03:09:38] mapped atoms in the reactants were not mapped in the products. +96: Randomness seeded to: 3307801759 +96: [23:38:06] atom 0 in product 0 has multiple charge specifications. +96: [23:38:06] Found a SCD/SED line with missing/empty SDT specification at line 34 +96: [23:38:06] Found a SCD/SED line with missing/empty SDT specification at line 36 +96: [23:38:06] Found a SCD/SED line with missing/empty SDT specification at line 38 +96: [23:38:06] Found a SCD/SED line with missing/empty SDT specification at line 40 +96: [23:38:06] Found a SCD/SED line with missing/empty SDT specification at line 42 +96: [23:38:06] Found a SCD/SED line with missing/empty SDT specification at line 87 +96: [23:38:06] Found a SCD/SED line with missing/empty SDT specification at line 89 +96: [23:38:06] Found a SCD/SED line with missing/empty SDT specification at line 91 +96: [23:38:06] Found a SCD/SED line with missing/empty SDT specification at line 93 +96: [23:38:06] Found a SCD/SED line with missing/empty SDT specification at line 95 +96: [23:38:06] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [03:09:38] mapped atoms in the reactants were not mapped in the products. +96: [23:38:06] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [03:09:38] SMARTS Parse Error: unclosed ring for input: 'CC1' -96: [03:09:38] SMILES Parse Error: unclosed ring for input: 'CC1' -96: [03:09:38] mapped atoms in the reactants were not mapped in the products. +96: [23:38:06] SMARTS Parse Error: unclosed ring for input: 'CC1' +96: [23:38:06] SMILES Parse Error: unclosed ring for input: 'CC1' +96: [23:38:06] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [03:09:38] product atom-mapping number 2 not found in reactants. -96: [03:09:38] mapped atoms in the reactants were not mapped in the products. +96: [23:38:06] product atom-mapping number 2 not found in reactants. +96: [23:38:06] mapped atoms in the reactants were not mapped in the products. 96: unmapped numbers are: 2 -96: [03:09:38] product atom-mapping number 2 not found in reactants. -96: [03:09:38] CX Extensions: Substance group hierarchy is not always preserved. -96: [03:09:38] CX Extensions: Substance group hierarchy is not always preserved. -96: [03:09:38] reactant 0 has no mapped atoms. -96: [03:09:38] product 0 has no mapped atoms. -96: [03:09:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [03:09:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [03:09:38] Explicit valence for atom # 1 O, 5, is greater than permitted +96: [23:38:06] product atom-mapping number 2 not found in reactants. +96: [23:38:06] CX Extensions: Substance group hierarchy is not always preserved. +96: [23:38:06] CX Extensions: Substance group hierarchy is not always preserved. +96: [23:38:06] reactant 0 has no mapped atoms. +96: [23:38:06] product 0 has no mapped atoms. +96: [23:38:06] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [23:38:06] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [23:38:06] Explicit valence for atom # 1 O, 5, is greater than permitted 96: =============================================================================== 96: All tests passed (722 assertions in 30 test cases) 96: - 85/236 Test #96: rxnTestCatch ........................... Passed 0.13 sec + 85/236 Test #96: rxnTestCatch ........................... Passed 0.07 sec test 97 Start 97: pyChemReactions 97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" 97: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 97: Test timeout computed to be: 1500 -40: [03:09:38] Finished -40: [03:09:38] testing stability w.r.t. renumbering. -40: [03:09:38] Finished -40: [03:09:38] testing smiles round-tripping. -69: [03:09:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:09:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:09:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:09:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:09:38] deprecated group abbreviation ignored on line 24 -69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -69: [03:09:38] -69: -69: **** -69: Post-condition Violation -69: Element 'Mv' not found -69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -69: Failed Expression: anum > -1 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 3# 0x0000FFFF87DD7F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x0000FFFF87DE5B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x0000FFFF87DE6A4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 9# 0x0000AAAAB479F77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x0000AAAAB4814944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x0000AAAAB4785C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x0000FFFF874A229C in /lib/aarch64-linux-gnu/libc.so.6 -69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 14# 0x0000AAAAB4785E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -40: [03:09:39] Finished -40: [03:09:39] testing github #1567: Non-canonical result from MolFragmentToSmiles() -40: [03:09:39] Finished -69: [03:09:39] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -69: [03:09:39] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. - 86/236 Test #40: hanoiTest .............................. Passed 4.56 sec -test 98 - Start 98: pyChemReactionEnumerations - -98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" -98: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -98: Test timeout computed to be: 1500 -69: ---------------------------------- -69: ---------------------------------- -69: [03:09:39] -69: -69: **** -69: Pre-condition Violation -69: rlabel out of range for MDL files -69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp -69: Failed Expression: rlabel >= 0 && rlabel < 100 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -69: 3# 0x0000AAAAB47AF23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x0000AAAAB48149A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x0000AAAAB4785C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x0000FFFF874A229C in /lib/aarch64-linux-gnu/libc.so.6 -69: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 8# 0x0000AAAAB4785E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -69: [03:09:39] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -97: ...[03:09:39] +89: [23:38:06] Explicit valence for atom # 2 O, 4, is greater than permitted +89: [23:38:06] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [23:38:06] Explicit valence for atom # 3 Be, 4, is greater than permitted +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +89: [23:38:06] Explicit valence for atom # 27 P, 6, is greater than permitted +97: ...[23:38:07] 97: 97: **** 97: Pre-condition Violation @@ -22771,7 +22716,7 @@ 97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 25# 0x0000FFFF9C092680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x0000FFFFBB6B2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -22782,17 +22727,17 @@ 97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x0000FFFF9A69C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x0000FFFF9A69C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x0000FFFF9A69C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x0000FFFF9A69C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x0000FFFF9A69C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x0000FFFFB9CBC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x0000FFFFB9CBC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x0000FFFFB9CBC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x0000FFFFB9CBC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x0000FFFFB9CBC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 46# 0x0000FFFF9C08F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x0000FFFFBB6AF25C 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# 0x0000000000536550 in /usr/bin/python3 @@ -22824,13 +22769,13 @@ 97: 75# 0x0000000000628F70 in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x0000FFFF9CBC229C in /lib/aarch64-linux-gnu/libc.so.6 +97: 78# 0x0000FFFFBC1E229C 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: [03:09:39] +97: [23:38:07] 97: 97: **** 97: Pre-condition Violation @@ -22864,7 +22809,7 @@ 97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so 97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 25# 0x0000FFFF9C092680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x0000FFFFBB6B2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -22875,17 +22820,17 @@ 97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x0000FFFF9A69C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x0000FFFF9A69C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x0000FFFF9A69C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x0000FFFF9A69C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x0000FFFF9A69C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x0000FFFFB9CBC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x0000FFFFB9CBC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x0000FFFFB9CBC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x0000FFFFB9CBC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x0000FFFFB9CBC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 46# 0x0000FFFF9C08F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x0000FFFFBB6AF25C 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# 0x0000000000536550 in /usr/bin/python3 @@ -22917,50 +22862,123 @@ 97: 75# 0x0000000000628F70 in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x0000FFFF9CBC229C in /lib/aarch64-linux-gnu/libc.so.6 +97: 78# 0x0000FFFFBC1E229C 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: -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 5.128s -12: -12: OK -97: .........[03:09:39] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [03:09:39] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [03:09:39] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [03:09:39] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: .[03:09:39] product atom-mapping number 1 found multiple times. -97: [03:09:39] product atom-mapping number 1 found multiple times. -97: ................[03:09:39] mapped atoms in the reactants were not mapped in the products. +97: .........[23:38:07] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [23:38:07] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [23:38:07] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [23:38:07] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: .[23:38:07] product atom-mapping number 1 found multiple times. +97: [23:38:07] product atom-mapping number 1 found multiple times. +97: ................[23:38:07] mapped atoms in the reactants were not mapped in the products. 97: unmapped numbers are: 3 -97: [03:09:39] mapped atoms in the reactants were not mapped in the products. +97: [23:38:07] 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: [03:09:39] mapped atoms in the reactants were not mapped in the products. +97: [23:38:07] mapped atoms in the reactants were not mapped in the products. 97: unmapped numbers are: 3 -97: ..[03:09:39] reactant 2 has no mapped atoms. -97: [03:09:39] reactant 2 has no mapped atoms. -97: [03:09:39] product 1 has no mapped atoms. - 87/236 Test #12: pyBV ................................... Passed 5.57 sec +97: ..[23:38:07] reactant 2 has no mapped atoms. +97: [23:38:07] reactant 2 has no mapped atoms. +97: [23:38:07] product 1 has no mapped atoms. +97: ........[23:38:07] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +97: [23:38:07] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +97: [23:38:07] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +97: [23:38:07] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +97: .[23:38:07] reactant atom-mapping number 1 found multiple times. +97: [23:38:07] product atom-mapping number 2 not found in reactants. +97: [23:38:07] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 4 +97: [23:38:07] product atom-mapping number 5 not found in reactants. +97: ........./build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> +97: png = open(fname, 'rb').read() +97: ResourceWarning: Enable tracemalloc to get the object allocation traceback +97: [23:38:07] Found a SCD/SED line with missing/empty SDT specification at line 34 +97: [23:38:07] Found a SCD/SED line with missing/empty SDT specification at line 36 +97: [23:38:07] Found a SCD/SED line with missing/empty SDT specification at line 38 +97: [23:38:07] Found a SCD/SED line with missing/empty SDT specification at line 40 +97: [23:38:07] Found a SCD/SED line with missing/empty SDT specification at line 42 +97: [23:38:07] Found a SCD/SED line with missing/empty SDT specification at line 87 +97: [23:38:07] Found a SCD/SED line with missing/empty SDT specification at line 89 +97: [23:38:07] Found a SCD/SED line with missing/empty SDT specification at line 91 +97: [23:38:07] Found a SCD/SED line with missing/empty SDT specification at line 93 +97: [23:38:07] Found a SCD/SED line with missing/empty SDT specification at line 95 +97: ..[23:38:07] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [23:38:07] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [23:38:07] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [23:38:07] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [23:38:07] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [23:38:07] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [23:38:07] reaction has no reactants +97: [23:38:07] reaction has no products +97: [23:38:07] initialization failed +97: [23:38:07] reaction has no reactants +97: [23:38:07] reaction has no products +97: .[23:38:07] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [23:38:07] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [23:38:07] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [23:38:07] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [23:38:07] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [23:38:07] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [23:38:07] reaction has no reactants +97: [23:38:07] reaction has no products +97: [23:38:07] initialization failed +97: [23:38:07] reaction has no reactants +97: [23:38:07] reaction has no products +97: . +97: ---------------------------------------------------------------------- +97: Ran 54 tests in 0.102s +97: +97: OK +97: ******************************************** +97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +97: + 86/236 Test #97: pyChemReactions ........................ Passed 0.44 sec +test 98 + Start 98: pyChemReactionEnumerations + +98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" +98: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +98: Test timeout computed to be: 1500 +89: [23:38:07] Explicit valence for atom # 9 N, 5, is greater than permitted +89: [23:38:07] Explicit valence for atom # 3 Al, 6, is greater than permitted +98: [23:38:07] == testCartesianProduct +89: [23:38:07] Explicit valence for atom # 4 Al, 6, is greater than permitted +98: .[23:38:07] == testEnumerateLibrary +98: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> +98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) +98: ResourceWarning: Enable tracemalloc to get the object allocation traceback +89: [23:38:07] Explicit valence for atom # 10 Si, 6, is greater than permitted +98: ..[23:38:07] == testRGroupState +98: .[23:38:07] == testRandomEnumerateAllBBsLibrary +98: ** [1, 1] +98: ** [0, 2] +98: ** [1, 0] +98: .[23:38:07] == testRandomEnumerateLibrary +98: .[23:38:07] == testRandomSample +98: .[23:38:07] == testRandomSampleAllBBs +98: .[23:38:07] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: [23:38:07] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: .[23:38:07] == testRemoveBadMatches +98: .[23:38:07] == testTimings +89: [23:38:07] Explicit valence for atom # 2 O, 4, is greater than permitted +89: [23:38:07] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [23:38:07] Explicit valence for atom # 3 Be, 4, is greater than permitted +89: [23:38:07] Explicit valence for atom # 27 P, 6, is greater than permitted +89: =============================================================================== +89: All tests passed (21562 assertions in 3 test cases) +89: + 87/236 Test #42: resMolSupplierTest ..................... Passed 4.36 sec + 88/236 Test #89: multithreadedSupplierCatchTest ......... Passed 2.42 sec test 99 Start 99: pyChemReactionSanitize 99: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" 99: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 99: Test timeout computed to be: 1500 -97: ........[03:09:39] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -97: [03:09:39] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -97: [03:09:39] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -97: [03:09:39] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -97: .[03:09:39] reactant atom-mapping number 1 found multiple times. -97: [03:09:39] product atom-mapping number 2 not found in reactants. -97: [03:09:39] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 4 -97: [03:09:39] product atom-mapping number 5 not found in reactants. - 88/236 Test #42: resMolSupplierTest ..................... Passed 4.92 sec test 100 Start 100: testChemTransforms @@ -22975,65 +22993,18 @@ 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 -97: ........./build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> -97: png = open(fname, 'rb').read() -97: ResourceWarning: Enable tracemalloc to get the object allocation traceback -100: [03:09:39] SMARTS Parse Error: syntax error while parsing: bar -100: [03:09:39] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -97: [03:09:39] Found a SCD/SED line with missing/empty SDT specification at line 34 -97: [03:09:39] Found a SCD/SED line with missing/empty SDT specification at line 36 -97: [03:09:39] Found a SCD/SED line with missing/empty SDT specification at line 38 -97: [03:09:39] Found a SCD/SED line with missing/empty SDT specification at line 40 -97: [03:09:39] Found a SCD/SED line with missing/empty SDT specification at line 42 -97: [03:09:39] Found a SCD/SED line with missing/empty SDT specification at line 87 -97: [03:09:39] Found a SCD/SED line with missing/empty SDT specification at line 89 -97: [03:09:39] Found a SCD/SED line with missing/empty SDT specification at line 91 -97: [03:09:39] Found a SCD/SED line with missing/empty SDT specification at line 93 -97: [03:09:39] Found a SCD/SED line with missing/empty SDT specification at line 95 -97: ..[03:09:39] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [03:09:39] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -97: [03:09:39] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [03:09:39] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [03:09:39] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [03:09:39] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [03:09:39] reaction has no reactants -97: [03:09:39] reaction has no products -97: [03:09:39] initialization failed -97: [03:09:39] reaction has no reactants -97: [03:09:39] reaction has no products -89: [03:09:39] Explicit valence for atom # 9 N, 5, is greater than permitted - 89/236 Test #100: testChemTransforms ..................... Passed 0.11 sec +100: [23:38:07] SMARTS Parse Error: syntax error while parsing: bar +100: [23:38:07] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' + 89/236 Test #100: testChemTransforms ..................... Passed 0.10 sec test 101 Start 101: chemTransformsTestCatch 101: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms 101: Test timeout computed to be: 1500 -97: .[03:09:39] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [03:09:39] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -97: [03:09:39] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [03:09:39] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [03:09:39] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [03:09:39] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -69: [03:09:39] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [03:09:39] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -97: [03:09:39] reaction has no reactants -97: [03:09:39] reaction has no products -97: [03:09:39] initialization failed -97: [03:09:39] reaction has no reactants -97: [03:09:39] reaction has no products -97: . -97: ---------------------------------------------------------------------- -97: Ran 54 tests in 0.321s -97: -97: OK -97: ******************************************** -97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -97: -98: [03:09:39] == testCartesianProduct -101: Randomness seeded to: 4052119854 -101: [03:09:39] Incomplete atom labelling, cannot make bond -101: [03:09:39] +101: Randomness seeded to: 1547570002 +101: [23:38:08] Incomplete atom labelling, cannot make bond +101: [23:38:08] 101: 101: **** 101: Invariant Violation @@ -23046,23 +23017,21 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAAE37E72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAE38352CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAE3835C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAE38360B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAE380A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAE380AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAE37DC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF955E229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAC2FB72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAC30052CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAC3005C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAC30060B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAC2FDA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAC2FDAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAC2FAC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFF9D85229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAE37DC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAC2FAC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -69: [03:09:39] Empty atom list: 'M ALS 1 0 F' on line 8. -98: .[03:09:39] == testEnumerateLibrary -101: [03:09:39] Incomplete atom labelling, cannot make bond -101: [03:09:39] +101: [23:38:08] Incomplete atom labelling, cannot make bond +101: [23:38:08] 101: 101: **** 101: Invariant Violation @@ -23075,31 +23044,21 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAAE37E72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAE38352CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAE3835C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAE38360B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAE380A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAE380AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAE37DC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF955E229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAC2FB72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAC30052CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAC3005C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAC30060B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAC2FDA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAC2FDAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAC2FAC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFF9D85229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAE37DC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAC2FAC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -98: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> -98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) -98: ResourceWarning: Enable tracemalloc to get the object allocation traceback - 90/236 Test #69: fileParsersTest1 ....................... Passed 4.15 sec -test 102 - Start 102: tautomerQueryTestCatch - -102: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch -102: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery -102: Test timeout computed to be: 1500 -101: [03:09:39] Incomplete atom labelling, cannot make bond -101: [03:09:39] +101: [23:38:08] Incomplete atom labelling, cannot make bond +101: [23:38:08] 101: 101: **** 101: Invariant Violation @@ -23112,24 +23071,23 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAAE37E72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAE38352CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAE3835C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAE38360B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAE380A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAE380AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAE37DC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF955E229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAC2FB72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAC30052CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAC3005C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAC30060B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAC2FDA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAC2FDAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAC2FAC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFF9D85229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAE37DC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAC2FAC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -101: [03:09:39] Incomplete atom labelling, cannot make bond -101: [03:09:39] Incomplete atom labelling, cannot make bond -101: [03:09:39] Incomplete atom labelling, cannot make bond -101: [03:09:39] +101: [23:38:08] Incomplete atom labelling, cannot make bond +101: [23:38:08] Incomplete atom labelling, cannot make bond +101: [23:38:08] Incomplete atom labelling, cannot make bond +101: [23:38:08] 101: 101: **** 101: Invariant Violation @@ -23142,21 +23100,21 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAAE37E72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAE38352CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAE3835C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAE38360B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAE380A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAE380AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAE37DC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF955E229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAC2FB72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAC30052CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAC3005C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAC30060B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAC2FDA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAC2FDAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAC2FAC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFF9D85229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAE37DC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAC2FAC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [03:09:39] Incomplete atom labelling, cannot make bond -101: [03:09:39] +101: [23:38:08] Incomplete atom labelling, cannot make bond +101: [23:38:08] 101: 101: **** 101: Invariant Violation @@ -23169,20 +23127,20 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAAE37E72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAAE38352CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAE3835C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAE38360B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAE380A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAE380AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAE37DC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFF955E229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAC2FB72AC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAC30052CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAC3005C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAC30060B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAC2FDA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAC2FDAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAC2FAC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFF9D85229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAAE37DC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAC2FAC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [03:09:39] +101: [23:38:08] 101: 101: **** 101: Invariant Violation @@ -23196,163 +23154,75 @@ 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 5# 0x0000AAAAE37DD6DC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAAE38352CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAAE3835C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAAE38360B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAAE380A638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAAE380AB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000AAAAE37DC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 12# 0x0000FFFF955E229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 5# 0x0000AAAAC2FAD6DC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAC30052CC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAC3005C80 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAC30060B4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAC2FDA638 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAC2FDAB84 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000AAAAC2FAC550 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 12# 0x0000FFFF9D85229C in /lib/aarch64-linux-gnu/libc.so.6 101: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 14# 0x0000AAAAE37DC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 14# 0x0000AAAAC2FAC630 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: =============================================================================== 101: All tests passed (675 assertions in 10 test cases) 101: - 91/236 Test #101: chemTransformsTestCatch ................ Passed 0.12 sec -test 103 - Start 103: pyTautomerQuery - -103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" -103: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap -103: Test timeout computed to be: 1500 -98: ..[03:09:39] == testRGroupState -98: .[03:09:39] == testRandomEnumerateAllBBsLibrary -98: ** [1, 1] -98: ** [0, 2] -98: ** [1, 0] -98: .[03:09:39] == testRandomEnumerateLibrary -98: .[03:09:39] == testRandomSample -98: .[03:09:39] == testRandomSampleAllBBs -98: .[03:09:39] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: [03:09:39] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: .[03:09:39] == testRemoveBadMatches -98: .[03:09:39] == testTimings - 92/236 Test #97: pyChemReactions ........................ Passed 1.20 sec -test 104 - Start 104: testSubgraphs1 - -104: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 -104: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs -104: Test timeout computed to be: 1500 -104: ----------------------- -104: Subgraph retrieval -104: Finished -104: ----------------------- -104: testSubgraphs2a -89: [03:09:39] Explicit valence for atom # 3 Al, 6, is greater than permitted -104: Finished -104: ----------------------- -104: testSubgraphs2 -89: [03:09:39] Explicit valence for atom # 4 Al, 6, is greater than permitted -102: Randomness seeded to: 3468753812 -102: =============================================================================== -102: All tests passed (93 assertions in 13 test cases) -102: -29: All 191 tests passed -89: [03:09:39] Explicit valence for atom # 10 Si, 6, is greater than permitted - 93/236 Test #102: tautomerQueryTestCatch ................. Passed 0.21 sec -test 105 - Start 105: testSubgraphs2 - -105: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 -105: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs -105: Test timeout computed to be: 1500 -104: Finished -104: ----------------------- -104: Path retrieval -104: Finished -104: ----------------------- -104: Path retrieval2 -104: Finished -104: ----------------------- -104: Unique Subgraph retrieval -104: Finished -104: ----------------------- -104: testUniqueSubgraphs2 -105: ----------------------- -105: Test1: pathToSubmol -105: Finished -105: ----------------------- -105: Test2: Atom Environments -105: Finished -105: ----------------------- -105: Test 3: Atom Environments (Extension) -105: Finished -105: ----------------------- -105: Testing github Issue103: stereochemistry and pathToSubmol -105: Finished -105: ----------------------- -105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) -105: Finished - 94/236 Test #105: testSubgraphs2 ......................... Passed 0.06 sec -test 106 - Start 106: subgraphsCatch - -106: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch -106: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs -106: Test timeout computed to be: 1500 -106: Randomness seeded to: 3248242338 -106: --------- -106: =============================================================================== -106: All tests passed (11 assertions in 1 test case) -106: - 95/236 Test #106: subgraphsCatch ......................... Passed 0.06 sec -test 107 - Start 107: filterCatalogTest + 90/236 Test #101: chemTransformsTestCatch ................ Passed 0.11 sec +test 102 + Start 102: tautomerQueryTestCatch -107: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest -107: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog -107: Test timeout computed to be: 1500 -99: .[03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: .[03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. +102: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch +102: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery +102: Test timeout computed to be: 1500 +99: .[23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: .[23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. 99: () 99: ******************************************** 99: $RXN @@ -23716,16 +23586,16 @@ 99: 1 2 1 0 99: M ISO 2 1 1 2 2 99: M END -99: [03:09:40] reactant 0 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] product 0 has no mapped atoms. -99: [03:09:40] Could not find RLabel mapping for atom: 0 in template: 1 -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. -99: [03:09:40] reactant 1 has no mapped atoms. +99: [23:38:08] reactant 0 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] product 0 has no mapped atoms. +99: [23:38:08] Could not find RLabel mapping for atom: 0 in template: 1 +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. +99: [23:38:08] reactant 1 has no mapped atoms. 99: .. 99: ---------------------------------------------------------------------- -99: Ran 4 tests in 0.045s +99: Ran 4 tests in 0.021s 99: 99: OK 99: @@ -23782,7 +23652,188 @@ 99: M END 99: 99: $RXN Failed +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +102: Randomness seeded to: 3351768684 +102: =============================================================================== +102: All tests passed (93 assertions in 13 test cases) +102: + 91/236 Test #102: tautomerQueryTestCatch ................. Passed 0.23 sec +test 103 + Start 103: pyTautomerQuery + +103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" +103: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap +103: Test timeout computed to be: 1500 +29: All 191 tests passed + 92/236 Test #99: pyChemReactionSanitize ................. Passed 0.48 sec +test 104 + Start 104: testSubgraphs1 + +104: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 +104: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs +104: Test timeout computed to be: 1500 +104: ----------------------- +104: Subgraph retrieval +104: Finished +104: ----------------------- +104: testSubgraphs2a 29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +104: Finished +104: ----------------------- +104: testSubgraphs2 +40: [23:38:08] done: 500000 +40: [23:38:08] Done +69: [23:38:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [23:38:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [23:38:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [23:38:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [23:38:08] deprecated group abbreviation ignored on line 24 +69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +69: [23:38:08] +69: +69: **** +69: Post-condition Violation +69: Element 'Mv' not found +69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +69: Failed Expression: anum > -1 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 3# 0x0000FFFF95897F24 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x0000FFFF958A5B20 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x0000FFFF958A6A4C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 9# 0x0000AAAAD372F77C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x0000AAAAD37A4944 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x0000AAAAD3715C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x0000FFFF94F6229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +69: 14# 0x0000AAAAD3715E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +40: [23:38:08] Testing hanoi with a functor. +104: Finished +104: ----------------------- +104: Path retrieval +104: Finished +104: ----------------------- +104: Path retrieval2 +104: Finished +104: ----------------------- +104: Unique Subgraph retrieval +104: Finished +104: ----------------------- +104: testUniqueSubgraphs2 +40: [23:38:08] Done +40: [23:38:08] Testing basic partition refinement. +40: [23:38:08] Done +40: [23:38:08] Testing partition refinement with neighbors. +40: [23:38:08] Done +40: [23:38:08] testing canonicalization via tie breaking. +40: [23:38:08] Done +40: [23:38:08] testing canonicalization using the wrapper. +40: [23:38:08] Done +40: [23:38:08] testing some specific ordering problems +40: [23:38:08] Finished +40: [23:38:08] testing chiral invariants. +40: [23:38:08] Finished +40: [23:38:08] testing unique ranks in w.r.t. renumbering. +40: [23:38:08] Finished +40: [23:38:08] testing mol fragments. +40: [23:38:08] Finished +40: [23:38:08] testing protein round-tripping. +103: ..... +103: ---------------------------------------------------------------------- +103: Ran 5 tests in 0.072s +103: +103: OK +69: [23:38:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: [23:38:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. + 93/236 Test #103: pyTautomerQuery ........................ Passed 0.66 sec +test 105 + Start 105: testSubgraphs2 + +105: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 +105: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs +105: Test timeout computed to be: 1500 +105: ----------------------- +105: Test1: pathToSubmol +105: Finished +105: ----------------------- +105: Test2: Atom Environments +105: Finished +105: ----------------------- +105: Test 3: Atom Environments (Extension) +105: Finished +105: ----------------------- +105: Testing github Issue103: stereochemistry and pathToSubmol +105: Finished +105: ----------------------- +105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) +105: Finished + 94/236 Test #105: testSubgraphs2 ......................... Passed 0.03 sec +test 106 + Start 106: subgraphsCatch + +106: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch +106: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs +106: Test timeout computed to be: 1500 +106: Randomness seeded to: 3765921519 +106: --------- +106: =============================================================================== +106: All tests passed (11 assertions in 1 test case) +106: + 95/236 Test #106: subgraphsCatch ......................... Passed 0.03 sec +test 107 + Start 107: filterCatalogTest + +107: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest +107: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog +107: Test timeout computed to be: 1500 +69: ---------------------------------- +69: ---------------------------------- +69: [23:38:09] +69: +69: **** +69: Pre-condition Violation +69: rlabel out of range for MDL files +69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp +69: Failed Expression: rlabel >= 0 && rlabel < 100 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +69: 3# 0x0000AAAAD373F23C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x0000AAAAD37A49A4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x0000AAAAD3715C6C in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x0000FFFF94F6229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +69: 8# 0x0000AAAAD3715E30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +69: [23:38:09] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +104: Finished +104: ----------------------- +104: testRootedSubgraphs +104: Finished +104: ----------------------- +104: testRootedPaths +104: Finished + 96/236 Test #104: testSubgraphs1 ......................... Passed 0.88 sec +test 108 + Start 108: pyFilterCatalog + +108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" +108: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap +108: Test timeout computed to be: 1500 107: Warning: molecule failed filter 107: Warning: molecule failed filter: reason hzone_phenol_A(479) 107: v = { @@ -23810,7 +23861,6 @@ 107: 9,21}, 107: } 107: Warning: molecule failed filter -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... 107: Warning: molecule failed filter: reason cyano_imine_B(17) 107: v = { 107: 0,11}, @@ -23872,133 +23922,413 @@ 107: 10,15}, 107: 11,16}, 107: } -103: ..... -103: ---------------------------------------------------------------------- -103: Ran 5 tests in 0.049s -103: -103: OK -104: Finished -104: ----------------------- -104: testRootedSubgraphs -104: Finished -104: ----------------------- -104: testRootedPaths -104: Finished - 96/236 Test #104: testSubgraphs1 ......................... Passed 0.37 sec -test 108 - Start 108: pyFilterCatalog - -108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" -108: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap -108: Test timeout computed to be: 1500 - 97/236 Test #99: pyChemReactionSanitize ................. Passed 0.79 sec +108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +98: . +98: ---------------------------------------------------------------------- +98: Ran 11 tests in 1.958s +98: +98: OK +98: True +98: == CartesianProductStrategy CartesianProductStrategy +98: 197 out of 300 +98: 0 6 out of 10 +98: 1 3 out of 5 +98: 2 4 out of 6 +98: 198 out of 300 +98: 0 10 out of 10 +98: 1 5 out of 5 +98: 2 6 out of 6 +98: Skipped 10000000 in 0.13773655891418457 seconds +98: Skipped 10000000 in 1.0853815078735352 seconds +98: Skipped 10000000 in 0.27004265785217285 seconds +69: [23:38:09] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [23:38:09] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' + 97/236 Test #107: filterCatalogTest ...................... Passed 0.67 sec test 109 Start 109: testFragCatalog 109: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog 109: Test timeout computed to be: 1500 -89: [03:09:40] Explicit valence for atom # 2 O, 4, is greater than permitted -89: [03:09:40] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [03:09:40] Explicit valence for atom # 3 Be, 4, is greater than permitted - 98/236 Test #107: filterCatalogTest ...................... Passed 0.29 sec +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 6.631s +12: +12: OK + 98/236 Test #98: pyChemReactionEnumerations ............. Passed 2.56 sec test 110 Start 110: pyFragCatalog 110: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/rough_test.py" 110: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 110: Test timeout computed to be: 1500 -89: [03:09:40] Explicit valence for atom # 27 P, 6, is greater than permitted - 99/236 Test #103: pyTautomerQuery ........................ Passed 0.58 sec +109: 21 +69: [23:38:09] Empty atom list: 'M ALS 1 0 F' on line 8. + 99/236 Test #69: fileParsersTest1 ....................... Passed 5.36 sec test 111 Start 111: testDescriptors 111: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors 111: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 -109: 21 -111: [03:09:40] ------------------------------------- -111: [03:09:40] Test Crippen parameter acquisition. -111: [03:09:40] done -111: [03:09:40] ------------------------------------- -111: [03:09:40] Test Crippen calculation. -111: [03:09:40] done -111: [03:09:40] ------------------------------------- -111: [03:09:40] Test Issue262: problems with Crippen calculation from pickles. -111: [03:09:40] done -111: [03:09:40] ------------------------------------- -111: [03:09:40] Test AMW calculation. -111: [03:09:40] done -111: [03:09:40] ------------------------------------- -111: [03:09:40] Test Exact MW calculation. -111: [03:09:40] done -111: [03:09:40] ------------------------------------- -111: [03:09:40] Test Labute ASA descriptors. -111: [03:09:40] done -111: [03:09:40] ------------------------------------- -111: [03:09:40] Test TPSA descriptors. -111: [03:09:40] done -111: [03:09:40] ------------------------------------- -111: [03:09:40] Test Lipinski parameters. -111: [03:09:40] done -111: [03:09:40] ------------------------------------- -111: [03:09:40] Test VSA descriptors. -111: [03:09:40] done -111: [03:09:40] ------------------------------------- -111: [03:09:40] Test molecular formula calculation. -111: [03:09:40] done -111: [03:09:40] ------------------------------------- -111: [03:09:40] Test Issue 3415534. -111: [03:09:40] done -111: [03:09:40] ------------------------------------- -111: [03:09:40] Test Issue3433771: Bad definition for Crippen atom type O11. -111: [03:09:40] done -111: [03:09:40] ------------------------------------- -111: [03:09:40] Test multithreading -111: reading molecules -111: processing -111: launch :0 -111: launch :1 -111: launch :2 -111: launch :3 -110: ......... -110: ---------------------------------------------------------------------- -110: Ran 9 tests in 0.073s -110: -110: OK -108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -89: [03:09:40] Explicit valence for atom # 9 N, 5, is greater than permitted -100/236 Test #110: pyFragCatalog .......................... Passed 0.52 sec +111: [23:38:09] ------------------------------------- +111: [23:38:09] Test Crippen parameter acquisition. +100/236 Test #12: pyBV ................................... Passed 7.06 sec test 112 Start 112: testAUTOCORR2D 112: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 112: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 -112: [03:09:40] ---------------------------- +111: [23:38:09] done +111: [23:38:09] ------------------------------------- +111: [23:38:09] Test Crippen calculation. +111: [23:38:09] done +111: [23:38:09] ------------------------------------- +111: [23:38:09] Test Issue262: problems with Crippen calculation from pickles. +111: [23:38:09] done +111: [23:38:09] ------------------------------------- +111: [23:38:09] Test AMW calculation. +111: [23:38:09] done +111: [23:38:09] ------------------------------------- +111: [23:38:09] Test Exact MW calculation. +111: [23:38:09] done +111: [23:38:09] ------------------------------------- +111: [23:38:09] Test Labute ASA descriptors. +111: [23:38:09] done +111: [23:38:09] ------------------------------------- +111: [23:38:09] Test TPSA descriptors. +112: [23:38:09] ---------------------------- 112: start test autocorr2D -89: [03:09:40] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [03:09:41] Explicit valence for atom # 4 Al, 6, is greater than permitted -89: [03:09:41] Explicit valence for atom # 10 Si, 6, is greater than permitted -98: . -98: ---------------------------------------------------------------------- -98: Ran 11 tests in 1.454s -98: -98: OK -98: True -98: == CartesianProductStrategy CartesianProductStrategy -98: 197 out of 300 -98: 0 6 out of 10 -98: 1 3 out of 5 -98: 2 4 out of 6 -98: 198 out of 300 -98: 0 10 out of 10 -98: 1 5 out of 5 -98: 2 6 out of 6 -98: Skipped 10000000 in 0.07551288604736328 seconds -98: Skipped 10000000 in 0.7298517227172852 seconds -98: Skipped 10000000 in 0.32042574882507324 seconds -109: [03:09:41] +111: [23:38:09] done +111: [23:38:09] ------------------------------------- +111: [23:38:09] Test Lipinski parameters. +40: [23:38:09] Finished +40: [23:38:09] testing stability w.r.t. renumbering. +40: [23:38:10] Finished +40: [23:38:10] testing smiles round-tripping. +108: .............[23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +108: [23:38:10] SMILES Parse Error: syntax error while parsing: --- +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] --- +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [23:38:10] dasfsadf +110: ......... +110: ---------------------------------------------------------------------- +110: Ran 9 tests in 0.040s +110: +110: OK +112: [23:38:10] done +112: [23:38:10] ------------------------------------- +112: [23:38:10] Test Github #3806: NaNs from AUTOCORR2D descriptor +112: [23:38:10] done +101/236 Test #110: pyFragCatalog .......................... Passed 0.46 sec +test 113 + Start 113: testATF + +113: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testATF +113: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +113: Test timeout computed to be: 1500 +102/236 Test #112: testAUTOCORR2D ......................... Passed 0.41 sec +test 114 + Start 114: testBCUT + +114: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testBCUT +114: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +114: Test timeout computed to be: 1500 +103/236 Test #113: testATF ................................ Passed 0.03 sec +test 115 + Start 115: testEEM + +115: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testEEM +115: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +115: Test timeout computed to be: 1500 +111: [23:38:10] done +111: [23:38:10] ------------------------------------- +111: [23:38:10] Test VSA descriptors. +111: [23:38:10] done +111: [23:38:10] ------------------------------------- +111: [23:38:10] Test molecular formula calculation. +111: [23:38:10] done +111: [23:38:10] ------------------------------------- +111: [23:38:10] Test Issue 3415534. +111: [23:38:10] done +111: [23:38:10] ------------------------------------- +111: [23:38:10] Test Issue3433771: Bad definition for Crippen atom type O11. +111: [23:38:10] done +111: [23:38:10] ------------------------------------- +111: [23:38:10] Test multithreading +111: reading molecules +114: [23:38:10] ------------------------------------- +114: [23:38:10] Basic BCUT tests. +108: .[23:38:10] SMILES Parse Error: syntax error while parsing: mydoghasfleas +108: [23:38:10] SMILES Parse Error: check for mistakes around position 1: +108: [23:38:10] mydoghasfleas +108: [23:38:10] ^ +108: [23:38:10] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +114: [23:38:10] done +114: [23:38:10] ------------------------------------- +114: [23:38:10] Larger BCUT tests. +111: processing +111: launch :0 +111: launch :1 +111: launch :2 +111: launch :3 +115: =>start test EEM +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 0 +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: ....... +108: ---------------------------------------------------------------------- +108: Ran 21 tests in 0.840s +108: +108: OK +108: (Five aromatic carbons And (Not any of Five aromatic carbons)) +108: (Five aromatic carbons Or (Not any of Five aromatic carbons)) +108: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) +108: ******************************************** +108: Testing: PAINS_A 2 +108: ******************************************** +108: Testing: PAINS_B 4 +108: ******************************************** +108: Testing: PAINS_C 8 +108: ******************************************** +108: Testing: PAINS 14 +108: (Not FilterMatcher) +108: Bar +108: Count 1 +108: ******************************************** +108: {'Cl,Br,I'} +108: 1 +108: 2 +108: running +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +40: [23:38:10] Finished +40: [23:38:10] testing github #1567: Non-canonical result from MolFragmentToSmiles() +40: [23:38:10] Finished +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104/236 Test #40: hanoiTest .............................. Passed 6.95 sec +test 116 + Start 116: testPBF + +116: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testPBF +116: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +116: Test timeout computed to be: 1500 +109: [23:38:10] 109: 109: **** 109: Invariant Violation @@ -24009,17 +24339,17 @@ 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x0000FFFFBBEF1948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFF8E511948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000AAAAB70D7B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAAB70D4960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFFBB4C229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAAD8C87B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAAD8C84960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFF8DAE229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAAB70D4B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAAD8C84B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [03:09:41] +109: [23:38:10] 109: 109: **** 109: Invariant Violation @@ -24030,17 +24360,17 @@ 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x0000FFFFBBEF1948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFF8E511948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000AAAAB70D7B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAAB70D4960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFFBB4C229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAAD8C87B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAAD8C84960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFF8DAE229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAAB70D4B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAAD8C84B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [03:09:41] +109: [23:38:10] 109: 109: **** 109: Invariant Violation @@ -24051,863 +24381,567 @@ 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x0000FFFFBBEF1948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFF8E511948 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000AAAAB70D7B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAAB70D4960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFFBB4C229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAAD8C87B08 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAAD8C84960 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFF8DAE229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAAB70D4B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAAD8C84B30 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -101/236 Test #109: testFragCatalog ........................ Passed 1.02 sec -test 113 - Start 113: testATF - -113: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testATF -113: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -113: Test timeout computed to be: 1500 -102/236 Test #113: testATF ................................ Passed 0.05 sec -test 114 - Start 114: testBCUT - -114: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testBCUT -114: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -114: Test timeout computed to be: 1500 -89: [03:09:41] Explicit valence for atom # 2 O, 4, is greater than permitted -89: [03:09:41] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [03:09:41] Explicit valence for atom # 3 Be, 4, is greater than permitted -103/236 Test #98: pyChemReactionEnumerations ............. Passed 2.23 sec -test 115 - Start 115: testEEM - -115: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testEEM -115: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -115: Test timeout computed to be: 1500 -114: [03:09:41] ------------------------------------- -114: [03:09:41] Basic BCUT tests. -115: =>start test EEM -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 0 -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:09:41] Explicit valence for atom # 27 P, 6, is greater than permitted -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -114: [03:09:41] done -114: [03:09:41] ------------------------------------- -114: [03:09:41] Larger BCUT tests. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: =============================================================================== -89: All tests passed (21562 assertions in 3 test cases) -89: -104/236 Test #89: multithreadedSupplierCatchTest ......... Passed 4.21 sec -test 116 - Start 116: testPBF - -116: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testPBF -116: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -116: Test timeout computed to be: 1500 -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [03:09:41] ------------------------------------- -116: [03:09:41] Basic PBF tests. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [03:09:41] done -112: [03:09:41] ------------------------------------- -112: [03:09:41] Test Github #3806: NaNs from AUTOCORR2D descriptor -112: [03:09:41] done -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -105/236 Test #112: testAUTOCORR2D ......................... Passed 0.72 sec +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +105/236 Test #109: testFragCatalog ........................ Passed 0.70 sec test 117 Start 117: testRDFcustom 117: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom 117: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 117: Test timeout computed to be: 1500 -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 100 -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 200 -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [03:09:41] done -116: [03:09:41] ------------------------------------- -116: [03:09:41] PBF edge cases. -116: [03:09:41] done -106/236 Test #116: testPBF ................................ Passed 0.30 sec +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [23:38:10] ------------------------------------- +116: [23:38:10] Basic PBF tests. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +106/236 Test #108: pyFilterCatalog ........................ Passed 1.22 sec test 118 Start 118: testRDF 118: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDF 118: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 118: Test timeout computed to be: 1500 -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 300 -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 400 -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:09:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: Elapsed time: 0.601074 s -115: Errors:0 -115: [03:09:41] test on : 500 molecules done -107/236 Test #115: testEEM ................................ Passed 0.63 sec +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 100 +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 200 +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [23:38:10] done +116: [23:38:10] ------------------------------------- +116: [23:38:10] PBF edge cases. +116: [23:38:10] done +107/236 Test #116: testPBF ................................ Passed 0.35 sec test 119 Start 119: testMORSE 119: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testMORSE 119: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 119: Test timeout computed to be: 1500 -108: .............[03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -108: [03:09:42] SMILES Parse Error: syntax error while parsing: --- -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] --- -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:09:42] dasfsadf -74: [03:09:42] Finished: testSmiCorrectness() -74: [03:09:42] ----------------------------------------- -74: -74: [03:09:42] -74: ----------------------------------------- -117: =>start test rdf custom -117: [03:09:42] test on : 365 molecules done -108: .[03:09:42] SMILES Parse Error: syntax error while parsing: mydoghasfleas -108: [03:09:42] SMILES Parse Error: check for mistakes around position 1: -108: [03:09:42] mydoghasfleas -108: [03:09:42] ^ -108: [03:09:42] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' -74: [03:09:42] Spurious data before the first property will be ignored -74: [03:09:42] Property will be truncated after the first blank line -74: [03:09:42] Property will be truncated after the first blank line -74: [03:09:42] Property will be truncated after the first blank line -118: =>start test rdf -118: [03:09:42] test on : 365 molecules done -108/236 Test #118: testRDF ................................ Passed 0.62 sec +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [23:38:10] ------------------------------------- +114: [23:38:10] Test empty molecule BCUT. +108/236 Test #114: testBCUT ............................... Passed 0.68 sec test 120 Start 120: test3D 120: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/test3D 120: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 120: Test timeout computed to be: 1500 -120: [03:09:42] ------------------------------------- -120: [03:09:42] Basic PMI tests. -108: ....... -108: ---------------------------------------------------------------------- -108: Ran 21 tests in 1.675s -108: -108: OK -108: (Five aromatic carbons And (Not any of Five aromatic carbons)) -108: (Five aromatic carbons Or (Not any of Five aromatic carbons)) -108: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) -108: ******************************************** -108: Testing: PAINS_A 2 -108: ******************************************** -108: Testing: PAINS_B 4 -108: ******************************************** -108: Testing: PAINS_C 8 -108: ******************************************** -108: Testing: PAINS 14 -108: (Not FilterMatcher) -108: Bar -108: Count 1 -108: ******************************************** -108: {'Cl,Br,I'} -108: 1 -108: 2 -108: running -119: =>start test MORSE -119: =>read file -119: [03:09:42] test on : 365 molecules done -109/236 Test #119: testMORSE .............................. Passed 0.49 sec +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +118: =>start test rdf +118: [23:38:10] test on : 365 molecules done +109/236 Test #118: testRDF ................................ Passed 0.46 sec test 121 Start 121: testWHIM 121: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testWHIM 121: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 121: Test timeout computed to be: 1500 -114: [03:09:42] ------------------------------------- -114: [03:09:42] Test empty molecule BCUT. -110/236 Test #114: testBCUT ............................... Passed 1.18 sec +120: [23:38:10] ------------------------------------- +120: [23:38:10] Basic PMI tests. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 300 +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +117: =>start test rdf custom +117: [23:38:11] test on : 365 molecules done +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +120: [23:38:11] done +120: [23:38:11] ------------------------------------- +120: [23:38:11] More PMI/NPR tests. +120: [23:38:11] done +120: [23:38:11] ------------------------------------- +120: [23:38:11] Basic NPR tests. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 400 +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +120: [23:38:11] done +120: [23:38:11] ------------------------------------- +120: [23:38:11] PMI edge cases. +120: [23:38:11] done +120: [23:38:11] ------------------------------------- +120: [23:38:11] NPR edge cases. +120: [23:38:11] done +120: [23:38:11] ------------------------------------- +120: [23:38:11] 3D descriptors. +120: [23:38:11] done +120: [23:38:11] ------------------------------------- +120: [23:38:11] 3D descriptor edge cases. +120: [23:38:11] done +120: [23:38:11] ------------------------------------- +120: [23:38:11] Inertial shape factor. +120: [23:38:11] done +110/236 Test #120: test3D ................................. Passed 0.37 sec test 122 Start 122: testGETAWAY 122: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 122: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 122: Test timeout computed to be: 1500 -111/236 Test #108: pyFilterCatalog ........................ Passed 2.45 sec +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [23:38:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: Elapsed time: 1.06166 s +115: Errors:0 +115: [23:38:11] test on : 500 molecules done +111/236 Test #115: testEEM ................................ Passed 1.11 sec test 123 Start 123: testAUTOCORR3D 123: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 123: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 123: Test timeout computed to be: 1500 -120: [03:09:42] done -120: [03:09:42] ------------------------------------- -120: [03:09:42] More PMI/NPR tests. -120: [03:09:42] done -120: [03:09:42] ------------------------------------- -120: [03:09:42] Basic NPR tests. -74: [03:09:42] Finished: testSDCorrectness() -74: [03:09:42] ----------------------------------------- -74: -112/236 Test #74: testMultithreadedMolSupplier ........... Passed 6.83 sec +121: =>start test WHIM +121: [23:38:11] test on : 365 molecules done +112/236 Test #121: testWHIM ............................... Passed 0.77 sec test 124 Start 124: testCoulombMat @@ -24916,23 +24950,23 @@ 124: Test timeout computed to be: 1500 124: ===================== Testing CoulombMat ======================= 124: CM test 1 mat Done -113/236 Test #124: testCoulombMat ......................... Passed 0.07 sec +113/236 Test #124: testCoulombMat ......................... Passed 0.05 sec test 125 Start 125: descriptorsTestCatch 125: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 125: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 125: Test timeout computed to be: 1500 -121: =>start test WHIM -121: [03:09:43] test on : 365 molecules done -114/236 Test #121: testWHIM ............................... Passed 0.53 sec +123: =>start test autocorr3D +123: [23:38:11] test on : 365 molecules done +114/236 Test #123: testAUTOCORR3D ......................... Passed 0.43 sec test 126 Start 126: pyMolDescriptors 126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 126: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 126: Test timeout computed to be: 1500 -125: Randomness seeded to: 3201596884 +125: Randomness seeded to: 3876930740 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 @@ -24940,33 +24974,141 @@ 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 -120: [03:09:43] done -120: [03:09:43] ------------------------------------- -120: [03:09:43] PMI edge cases. -120: [03:09:43] done -120: [03:09:43] ------------------------------------- -120: [03:09:43] NPR edge cases. -120: [03:09:43] done -120: [03:09:43] ------------------------------------- -120: [03:09:43] 3D descriptors. -120: [03:09:43] done -120: [03:09:43] ------------------------------------- -120: [03:09:43] 3D descriptor edge cases. -120: [03:09:43] done -120: [03:09:43] ------------------------------------- -120: [03:09:43] Inertial shape factor. -120: [03:09:43] done 125: Warning: Atom Count for residue GLU5A does not match expected count -115/236 Test #120: test3D ................................. Passed 0.82 sec +119: =>start test MORSE +119: =>read file +119: [23:38:12] test on : 365 molecules done +115/236 Test #119: testMORSE .............................. Passed 1.26 sec test 127 Start 127: pyMolDescriptors3D 127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/test3D.py" 127: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 127: Test timeout computed to be: 1500 -123: =>start test autocorr3D -123: [03:09:43] test on : 365 molecules done -116/236 Test #123: testAUTOCORR3D ......................... Passed 0.62 sec +117: =>start test morse custom +117: [23:38:12] test on : 365 molecules done +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: .[23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +126: ..[23:38:12] +126: +126: **** +126: Pre-condition Violation +126: Number of atom props not equal to number of atoms +126: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp +126: Failed Expression: atom_props.size() == num_atoms +126: ---------- +126: Stacktrace: +126: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +126: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +126: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitDescriptors.so.1 +126: 3# 0x0000FFFF90B2D0B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 4# 0x0000FFFF90B42370 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +126: 6# 0x0000FFFF949A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +126: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +126: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so +126: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so +126: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +126: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +126: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +126: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +126: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +126: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +126: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 17# 0x0000FFFF92F7C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 18# 0x0000FFFF92F7C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 19# 0x0000FFFF92F7C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 20# 0x0000FFFF92F7C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 21# 0x0000FFFF92F7C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +126: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +126: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +126: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +126: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +126: 27# 0x0000FFFF9499F25C 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# 0x0000000000536550 in /usr/bin/python3 +126: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 32# 0x00000000005D32E0 in /usr/bin/python3 +126: 33# 0x00000000006508D4 in /usr/bin/python3 +126: 34# _PyObject_MakeTpCall in /usr/bin/python3 +126: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 36# 0x0000000000536550 in /usr/bin/python3 +126: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 38# 0x00000000005D32E0 in /usr/bin/python3 +126: 39# 0x00000000006508D4 in /usr/bin/python3 +126: 40# _PyObject_MakeTpCall in /usr/bin/python3 +126: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 42# 0x0000000000536550 in /usr/bin/python3 +126: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 44# 0x00000000005D32E0 in /usr/bin/python3 +126: 45# 0x00000000006508D4 in /usr/bin/python3 +126: 46# _PyObject_MakeTpCall in /usr/bin/python3 +126: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 48# 0x0000000000508250 in /usr/bin/python3 +126: 49# _PyObject_MakeTpCall in /usr/bin/python3 +126: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 51# PyEval_EvalCode in /usr/bin/python3 +126: 52# 0x0000000000601BDC in /usr/bin/python3 +126: 53# 0x00000000005FC110 in /usr/bin/python3 +126: 54# 0x0000000000629A90 in /usr/bin/python3 +126: 55# 0x00000000006291D4 in /usr/bin/python3 +126: 56# 0x0000000000628F70 in /usr/bin/python3 +126: 57# Py_RunMain in /usr/bin/python3 +126: 58# Py_BytesMain in /usr/bin/python3 +126: 59# 0x0000FFFF952A229C in /lib/aarch64-linux-gnu/libc.so.6 +126: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +126: 61# _start in /usr/bin/python3 +126: ---------- +126: **** +126: +126: ...Warning: Atom Count for residue GLU5A does not match expected count +126: Warning: Atom Count for residue ASN39A does not match expected count +126: Warning: Atom Count for residue GLU53A does not match expected count +126: Warning: Atom Count for residue ARG64A does not match expected count +126: Warning: Atom Count for residue LYS80A does not match expected count +125: Warning: Atom Count for residue ASN39A does not match expected count +126: Warning: Atom Count for residue GLU150A does not match expected count +126: Warning: Atom Count for residue ASN157A does not match expected count +127: ........ +127: ---------------------------------------------------------------------- +127: Ran 8 tests in 0.202s +127: +127: OK +126: Warning: Atom Count for residue GLU5A does not match expected count +116/236 Test #127: pyMolDescriptors3D ..................... Passed 0.79 sec test 128 Start 128: testFingerprints @@ -25324,6 +25466,8 @@ 128: 128: ------------------- 128: +117: =>start test AUTOCORR3D custom +117: [23:38:12] test on : 365 molecules done 128: SMI: c1(O)c2c(cc(O)n1)[nH]cn2 128: Atoms: 128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 @@ -25456,803 +25600,687 @@ 128: 128: ------------------- 128: -117: =>start test morse custom -117: [03:09:43] test on : 365 molecules done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Morgan Fingerprints. -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Morgan Fingerprints using fromAtoms argument. -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Morgan Fingerprints as bit vects. -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Morgan Fingerprints with feature invariants. -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test additional Morgan fingerprints options. -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Atom Codes. -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Atom Pairs. -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Atom Pairs part 2. -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Topological Torsions. -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Bulk Topological Torsions. -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: .[03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -126: ..[03:09:43] -126: -126: **** -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: Pre-condition Violation -126: Number of atom props not equal to number of atoms -126: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp -126: Failed Expression: atom_props.size() == num_atoms -126: ---------- -126: Stacktrace: -126: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -126: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -126: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitDescriptors.so.1 -126: 3# 0x0000FFFF8BEED0B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -126: 4# 0x0000FFFF8BF02370 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -126: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -126: 6# 0x0000FFFF8FD62680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -126: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -126: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so -126: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so -126: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -126: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -126: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -126: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -126: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -126: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -126: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 17# 0x0000FFFF8E33C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 18# 0x0000FFFF8E33C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 19# 0x0000FFFF8E33C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 20# 0x0000FFFF8E33C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 21# 0x0000FFFF8E33C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -126: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -126: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -126: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -126: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -126: 27# 0x0000FFFF8FD5F25C 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# 0x0000000000536550 in /usr/bin/python3 -126: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 32# 0x00000000005D32E0 in /usr/bin/python3 -126: 33# 0x00000000006508D4 in /usr/bin/python3 -126: 34# _PyObject_MakeTpCall in /usr/bin/python3 -126: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 36# 0x0000000000536550 in /usr/bin/python3 -126: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 38# 0x00000000005D32E0 in /usr/bin/python3 -126: 39# 0x00000000006508D4 in /usr/bin/python3 -126: 40# _PyObject_MakeTpCall in /usr/bin/python3 -126: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 42# 0x0000000000536550 in /usr/bin/python3 -126: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 44# 0x00000000005D32E0 in /usr/bin/python3 -126: 45# 0x00000000006508D4 in /usr/bin/python3 -126: 46# _PyObject_MakeTpCall in /usr/bin/python3 -126: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 48# 0x0000000000508250 in /usr/bin/python3 -126: 49# _PyObject_MakeTpCall in /usr/bin/python3 -126: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 51# PyEval_EvalCode in /usr/bin/python3 -126: 52# 0x0000000000601BDC in /usr/bin/python3 -126: 53# 0x00000000005FC110 in /usr/bin/python3 -126: 54# 0x0000000000629A90 in /usr/bin/python3 -126: 55# 0x00000000006291D4 in /usr/bin/python3 -126: 56# 0x0000000000628F70 in /usr/bin/python3 -126: 57# Py_RunMain in /usr/bin/python3 -126: 58# Py_BytesMain in /usr/bin/python3 -126: 59# 0x0000FFFF9066229C in /lib/aarch64-linux-gnu/libc.so.6 -126: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -126: 61# _start in /usr/bin/python3 -126: ---------- -126: **** -126: -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Hashed Atom Pairs. -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Hashed torsions. -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Rooted Atom Pairs. -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test ignoring atoms in Atom Pairs. -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Rooted Topological Torsions. -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test ignoring atoms in Topological Torsions. -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test atom info from morgan fingerprints. -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test atom info from morgan fingerprints including Info Redundant Environments. -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] ------------------------------------- -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] ------------------------------------- -128: [03:09:43] ------------------------------------- -128: [03:09:43] ------------------------------------- -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Atom Pairs including info about chirality. -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test Topological Torsions including info about chirality. -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test GitHub Issue 25: fingerprint backwards compatibility. -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test GitHub Issue 151: PatternFingerprint problems -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 -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test 3D atom pairs. -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -128: [03:09:43] done -128: [03:09:43] ------------------------------------- -128: [03:09:43] Test multithreading with the pattern FP +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test Morgan Fingerprints. +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test Morgan Fingerprints using fromAtoms argument. +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test Morgan Fingerprints as bit vects. +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test Morgan Fingerprints with feature invariants. +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test additional Morgan fingerprints options. +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test Atom Codes. +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test Atom Pairs. +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test Atom Pairs part 2. +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test Topological Torsions. +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test Bulk Topological Torsions. +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +125: Warning: Atom Count for residue GLU53A does not match expected count +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test Hashed Atom Pairs. +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test Hashed torsions. +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test Rooted Atom Pairs. +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test ignoring atoms in Atom Pairs. +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test Rooted Topological Torsions. +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test ignoring atoms in Topological Torsions. +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test atom info from morgan fingerprints. +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] Test atom info from morgan fingerprints including Info Redundant Environments. +128: [23:38:12] done +128: [23:38:12] ------------------------------------- +128: [23:38:12] ------------------------------------- +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:12] ------------------------------------- +128: [23:38:13] ------------------------------------- +128: [23:38:13] ------------------------------------- +128: [23:38:13] ------------------------------------- +128: [23:38:13] Test Atom Pairs including info about chirality. +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] done +128: [23:38:13] ------------------------------------- +128: [23:38:13] Test Topological Torsions including info about chirality. +128: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:13] done +128: [23:38:13] ------------------------------------- +128: [23:38:13] Test GitHub Issue 25: fingerprint backwards compatibility. +128: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] done +128: [23:38:13] ------------------------------------- +128: [23:38:13] Test GitHub Issue 151: PatternFingerprint problems +128: [23:38:13] done +128: [23:38:13] ------------------------------------- +128: [23:38:13] Test 3D atom pairs. +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:13] done +128: [23:38:13] ------------------------------------- +128: [23:38:13] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +128: [23:38:13] done +128: [23:38:13] ------------------------------------- +128: [23:38:13] Test multithreading with the pattern FP 128: reading molecules -126: Warning: Atom Count for residue ARG64A does not match expected count -126: Warning: Atom Count for residue LYS80A does not match expected count -126: Warning: Atom Count for residue GLU150A does not match expected count -126: Warning: Atom Count for residue ASN157A does not match expected count -125: Warning: Atom Count for residue ASN39A does not match expected count 128: pass 1 128: launch :0 128: launch :1 128: launch :2 128: launch :3 -126: Warning: Atom Count for residue GLU5A does not match expected count -117: =>start test AUTOCORR3D custom -117: [03:09:43] test on : 365 molecules done -125: Warning: Atom Count for residue GLU53A does not match expected count -128: pass 2 -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test Issue252: Bad definitions for Crippen atom types. -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test calculation of ChiVs. -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test calculation of ChiNs. -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test calculation of HallKierAlpha. -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test calculation of Kappa1. -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test calculation of Kappa2. 125: Warning: Atom Count for residue ARG64A does not match expected count -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test calculation of Kappa3. -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test Crippen atom type calculations. -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test ring descriptors -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test other count descriptors. -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test MQN -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test GitHub Issue 56. -111: [03:09:43] WARNING: not removing hydrogen atom without neighbors -111: [03:09:43] WARNING: not removing hydrogen atom without neighbors -111: [03:09:43] WARNING: not removing hydrogen atom without neighbors -111: [03:09:43] WARNING: not removing hydrogen atom without neighbors -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test Github92: Bad Crippen atom type for pyrrole H. -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test Github362: order dependence in Kier-Hall descriptors. -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test calculation of spiro and bridgehead counts. -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test Github694: ExactMolWt ignoring the mass of the electron -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Testing Properties and KitchenSink -111: [03:09:43] ---Caught keyerror (bad property name)--- -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test USR Descriptor -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test Github #1973: support P and S terms for TPSA calculation -111: [03:09:43] done -111: [03:09:43] ------------------------------------- -111: [03:09:43] Test Github #2948: Empty molecule has non-zero LabuteASA -111: [03:09:43] done -117/236 Test #111: testDescriptors ........................ Passed 3.61 sec +117: =>start test 2 WHIM custom +117: [23:38:13] test on : 365 molecules done +122: =>start test GETAWAY +122: [23:38:13] test on : 365 molecules done +117/236 Test #122: testGETAWAY ............................ Passed 1.83 sec test 129 Start 129: testMHFPFingerprint 129: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint 129: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 129: Test timeout computed to be: 1500 -117: =>start test 2 WHIM custom -117: [03:09:43] test on : 365 molecules done -127: ........ -127: ---------------------------------------------------------------------- -127: Ran 8 tests in 0.255s -127: -127: OK -129: [03:09:43] ------------------------------------- -129: [03:09:43] Test MHFP fingerprint encoder initialization -129: [03:09:44] done -129: [03:09:44] ------------------------------------- -129: [03:09:44] Test MHFP shingling creation -129: [03:09:44] done -129: [03:09:44] ------------------------------------- -129: [03:09:44] Test MHFP hashing of string and uint arrays -129: [03:09:44] done -129: [03:09:44] ------------------------------------- -129: [03:09:44] Test SECFP fingerprint functionality -129: [03:09:44] done -118/236 Test #129: testMHFPFingerprint .................... Passed 0.11 sec +129: [23:38:13] ------------------------------------- +129: [23:38:13] Test MHFP fingerprint encoder initialization +129: [23:38:13] done +129: [23:38:13] ------------------------------------- +129: [23:38:13] Test MHFP shingling creation +129: [23:38:13] done +129: [23:38:13] ------------------------------------- +129: [23:38:13] Test MHFP hashing of string and uint arrays +129: [23:38:13] done +129: [23:38:13] ------------------------------------- +129: [23:38:13] Test SECFP fingerprint functionality +126: Warning: Atom Count for residue ASN39A does not match expected count +129: [23:38:13] done +118/236 Test #129: testMHFPFingerprint .................... Passed 0.09 sec test 130 Start 130: testFingerprintGenerators 130: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators 130: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 130: Test timeout computed to be: 1500 -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test atom-pair fp generator -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test atom-pair fp generator with different arguments -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -130: [03:09:44] DEPRECATION WARNING: please use AtomPairGenerator -130: [03:09:44] DEPRECATION WARNING: please use AtomPairGenerator -130: [03:09:44] DEPRECATION WARNING: please use AtomPairGenerator -130: [03:09:44] DEPRECATION WARNING: please use AtomPairGenerator -130: [03:09:44] DEPRECATION WARNING: please use AtomPairGenerator -130: [03:09:44] DEPRECATION WARNING: please use AtomPairGenerator -130: [03:09:44] DEPRECATION WARNING: please use AtomPairGenerator -130: [03:09:44] DEPRECATION WARNING: please use AtomPairGenerator -130: [03:09:44] DEPRECATION WARNING: please use AtomPairGenerator -130: [03:09:44] DEPRECATION WARNING: please use AtomPairGenerator -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test atom-pair additional output -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test Folded Atom Pairs. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test Rooted Atom Pairs. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test ignoring atoms in Atom Pairs. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test Atom Pairs including info about chirality. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test Morgan Fingerprints. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test morgan fp generator -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test Morgan Fingerprints using fromAtoms argument. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test Morgan Fingerprints as bit vects. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test Morgan Fingerprints with feature invariants. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test additional Morgan fingerprints options. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Single atoms setting radius 1 bits in Morgan fingerprints -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test different invariant generator combinations -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test invariant overriding -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test RDKit fp generator -119/236 Test #127: pyMolDescriptors3D ..................... Passed 0.96 sec +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test atom-pair fp generator +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test atom-pair fp generator with different arguments +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +130: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +128: pass 2 +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +130: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [23:38:13] DEPRECATION WARNING: please use AtomPairGenerator +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test atom-pair additional output +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test Folded Atom Pairs. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test Rooted Atom Pairs. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test ignoring atoms in Atom Pairs. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test Atom Pairs including info about chirality. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test Morgan Fingerprints. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test morgan fp generator +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test Morgan Fingerprints using fromAtoms argument. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test Morgan Fingerprints as bit vects. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test Morgan Fingerprints with feature invariants. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test additional Morgan fingerprints options. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Single atoms setting radius 1 bits in Morgan fingerprints +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test different invariant generator combinations +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test invariant overriding +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test RDKit fp generator +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test Issue252: Bad definitions for Crippen atom types. +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test calculation of ChiVs. +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test calculation of ChiNs. +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test calculation of HallKierAlpha. +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test calculation of Kappa1. +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test calculation of Kappa2. +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test calculation of Kappa3. +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test Crippen atom type calculations. +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test ring descriptors +117: =>start test 1 WHIM custom +117: [23:38:13] test on : 365 molecules done +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test other count descriptors. +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test MQN +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test GitHub Issue 56. +111: [23:38:13] WARNING: not removing hydrogen atom without neighbors +111: [23:38:13] WARNING: not removing hydrogen atom without neighbors +111: [23:38:13] WARNING: not removing hydrogen atom without neighbors +111: [23:38:13] WARNING: not removing hydrogen atom without neighbors +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test Github92: Bad Crippen atom type for pyrrole H. +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test Github362: order dependence in Kier-Hall descriptors. +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test calculation of spiro and bridgehead counts. +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test Github694: ExactMolWt ignoring the mass of the electron +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Testing Properties and KitchenSink +111: [23:38:13] ---Caught keyerror (bad property name)--- +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test USR Descriptor +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test Github #1973: support P and S terms for TPSA calculation +111: [23:38:13] done +111: [23:38:13] ------------------------------------- +111: [23:38:13] Test Github #2948: Empty molecule has non-zero LabuteASA +111: [23:38:13] done +119/236 Test #111: testDescriptors ........................ Passed 3.58 sec test 131 Start 131: fpTestCatch 131: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 131: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 131: Test timeout computed to be: 1500 -126: Warning: Atom Count for residue ASN39A does not match expected count -125: Warning: Atom Count for residue LYS80A does not match expected count -131: Randomness seeded to: 3863518422 +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +131: Randomness seeded to: 1218740313 131: =============================================================================== 131: All tests passed (188 assertions in 16 test cases) 131: -120/236 Test #131: fpTestCatch ............................ Passed 0.08 sec +120/236 Test #131: fpTestCatch ............................ Passed 0.02 sec test 132 Start 132: fpGenTestCatch 132: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 132: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 132: Test timeout computed to be: 1500 -117: =>start test 1 WHIM custom -117: [03:09:44] test on : 365 molecules done +125: Warning: Atom Count for residue LYS80A does not match expected count 126: Warning: Atom Count for residue GLU53A does not match expected count -132: Randomness seeded to: 2866810274 +132: Randomness seeded to: 4022890615 132: =============================================================================== 132: All tests passed (2737 assertions in 7 test cases) 132: -121/236 Test #132: fpGenTestCatch ......................... Passed 0.19 sec +121/236 Test #132: fpGenTestCatch ......................... Passed 0.17 sec test 133 Start 133: pyTestGenerator 133: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 133: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 133: Test timeout computed to be: 1500 +29: All 191 tests passed 126: Warning: Atom Count for residue ARG64A does not match expected count -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test unfolded version of RDKFP -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test topological torsion fp generator -130: [03:09:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:09:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:09:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:09:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:09:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:09:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:09:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:09:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:09:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:09:44] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test Topological Torsions. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test Folded torsions. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test Bulk Topological Torsions. -122: =>start test GETAWAY -122: [03:09:44] test on : 365 molecules done -122/236 Test #122: testGETAWAY ............................ Passed 2.10 sec +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test unfolded version of RDKFP +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test topological torsion fp generator +130: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [23:38:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test Topological Torsions. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test Folded torsions. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test Bulk Topological Torsions. +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... +74: [23:38:13] Finished: testSmiCorrectness() +74: [23:38:13] ----------------------------------------- +74: +74: [23:38:13] +74: ----------------------------------------- +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test Rooted Topological Torsions. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test ignoring atoms in Topological Torsions. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test Topological Torsions including info about chirality. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test GitHub Issue 25: fingerprint backwards compatibility. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +130: [23:38:13] done +130: [23:38:13] ------------------------------------- +130: [23:38:13] Test convenience and bulk fp calculation functions +74: [23:38:13] Spurious data before the first property will be ignored +74: [23:38:13] Property will be truncated after the first blank line +74: [23:38:13] Property will be truncated after the first blank line +74: [23:38:13] Property will be truncated after the first blank line +126: Warning: Atom Count for residue LYS80A does not match expected count +133: .............. +133: ---------------------------------------------------------------------- +133: Ran 14 tests in 0.254s +133: +133: OK +122/236 Test #133: pyTestGenerator ........................ Passed 0.89 sec test 134 Start 134: pyTestMHFP 134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 134: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 134: Test timeout computed to be: 1500 -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test Rooted Topological Torsions. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test ignoring atoms in Topological Torsions. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test Topological Torsions including info about chirality. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test GitHub Issue 25: fingerprint backwards compatibility. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -130: [03:09:44] done -130: [03:09:44] ------------------------------------- -130: [03:09:44] Test convenience and bulk fp calculation functions -126: Warning: Atom Count for residue LYS80A does not match expected count -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -134: .. -134: ---------------------------------------------------------------------- -134: Ran 2 tests in 0.054s -134: -134: OK -130: [03:09:45] done -130: [03:09:45] ------------------------------------- -130: [03:09:45] Test GitHub Issue #6958 -130: [03:09:45] DEPRECATION WARNING: please use AtomPairGenerator -123/236 Test #130: testFingerprintGenerators .............. Passed 1.11 sec +125: Warning: Atom Count for residue GLU150A does not match expected count +130: [23:38:14] done +130: [23:38:14] ------------------------------------- +130: [23:38:14] Test GitHub Issue #6958 +130: [23:38:14] DEPRECATION WARNING: please use AtomPairGenerator +123/236 Test #130: testFingerprintGenerators .............. Passed 1.32 sec test 135 Start 135: testPartialCharges 135: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 135: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges 135: Test timeout computed to be: 1500 -124/236 Test #135: testPartialCharges ..................... Passed 0.03 sec +125: Warning: Atom Count for residue ASN157A does not match expected count +124/236 Test #135: testPartialCharges ..................... Passed 0.05 sec test 136 Start 136: pyPartialCharges 136: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 136: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 136: Test timeout computed to be: 1500 -133: .............. -133: ---------------------------------------------------------------------- -133: Ran 14 tests in 0.265s -133: -133: OK -125/236 Test #134: pyTestMHFP ............................. Passed 0.63 sec +117: =>start test GETAWAY custom +117: [23:38:14] test on : 365 molecules done +125/236 Test #117: testRDFcustom .......................... Passed 4.17 sec test 137 Start 137: testMolTransforms 137: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 137: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 137: Test timeout computed to be: 1500 -125: Warning: Atom Count for residue GLU150A does not match expected count -29: All 191 tests passed 137: *********************************************************** 137: Testing MolTransforms 137: --------------------------------- @@ -26283,79 +26311,93 @@ 137: testWeightedCentroid 137: 137: *********************************************************** -126/236 Test #137: testMolTransforms ...................... Passed 0.10 sec +126/236 Test #137: testMolTransforms ...................... Passed 0.03 sec test 138 Start 138: molTransformsTestCatch 138: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch 138: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 138: Test timeout computed to be: 1500 -125: Warning: Atom Count for residue ASN157A does not match expected count -127/236 Test #133: pyTestGenerator ........................ Passed 0.98 sec +138: Randomness seeded to: 1855669205 +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-202503.1/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 139: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap 139: Test timeout computed to be: 1500 -138: Randomness seeded to: 3916810819 -138: =============================================================================== -138: All tests passed (4 assertions in 1 test case) -138: -128/236 Test #138: molTransformsTestCatch ................. Passed 0.07 sec +139: ........ +139: ---------------------------------------------------------------------- +139: Ran 8 tests in 0.026s +139: +139: OK +128/236 Test #139: pyMolTransforms ........................ Passed 0.27 sec test 140 Start 140: forceFieldHelpersCatch 140: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch 140: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers 140: Test timeout computed to be: 1500 -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -140: Randomness seeded to: 2781263318 -140: =============================================================================== -140: All tests passed (17 assertions in 2 test cases) -140: -129/236 Test #140: forceFieldHelpersCatch ................. Passed 0.10 sec +134: .. +134: ---------------------------------------------------------------------- +134: Ran 2 tests in 0.045s +134: +134: OK +74: [23:38:14] Finished: testSDCorrectness() +74: [23:38:14] ----------------------------------------- +74: +129/236 Test #74: testMultithreadedMolSupplier ........... Passed 10.05 sec test 141 Start 141: testMMFFForceFieldHelpers 141: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 141: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 141: Test timeout computed to be: 1500 -141: [03:09:45] ------------------------------------- -141: [03:09:45] Test MMFF atom types. -141: [03:09:45] done -141: [03:09:45] ------------------------------------- -141: [03:09:45] Testing MMFF builder tools. -141: [03:09:45] done -141: [03:09:45] ------------------------------------- -141: [03:09:45] Testing MMFF builder+minimization. -136: ....... -136: ---------------------------------------------------------------------- -136: Ran 7 tests in 0.109s -136: -136: OK -141: [03:09:45] done -141: [03:09:45] ------------------------------------- -141: [03:09:45] Testing Issue239. -130/236 Test #136: pyPartialCharges ....................... Passed 0.56 sec +141: [23:38:14] ------------------------------------- +141: [23:38:14] Test MMFF atom types. +140: Randomness seeded to: 2584867340 +140: =============================================================================== +140: All tests passed (17 assertions in 2 test cases) +140: +130/236 Test #140: forceFieldHelpersCatch ................. Passed 0.07 sec test 142 Start 142: testMMFFForceFieldHelpersMultiThread 142: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 142: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 142: Test timeout computed to be: 1500 -141: [03:09:45] done -141: [03:09:45] ------------------------------------- -141: [03:09:45] Testing calcEnergy with passed coords. -142: [03:09:45] ------------------------------------- -142: [03:09:45] Test MMFF multithreading -141: [03:09:45] done -141: [03:09:45] ------------------------------------- -141: [03:09:45] Testing calcGrad. -141: [03:09:45] done -141: [03:09:45] ------------------------------------- -141: [03:09:45] Testing Issue242. +141: [23:38:14] done +141: [23:38:14] ------------------------------------- +141: [23:38:14] Testing MMFF builder tools. +141: [23:38:15] done +141: [23:38:15] ------------------------------------- +141: [23:38:15] Testing MMFF builder+minimization. +131/236 Test #134: pyTestMHFP ............................. Passed 0.60 sec +test 143 + Start 143: testUFFForceFieldHelpers + +143: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers +143: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF +143: Test timeout computed to be: 1500 +142: [23:38:15] ------------------------------------- +142: [23:38:15] Test MMFF multithreading +143: [23:38:15] ------------------------------------- +143: [23:38:15] Test UFF atom labels. +143: [23:38:15] done +143: [23:38:15] ------------------------------------- +143: [23:38:15] Test UFF atom typer. +143: [23:38:15] done +143: [23:38:15] ------------------------------------- +143: [23:38:15] Testing UFF builder tools. +143: [23:38:15] done +143: [23:38:15] ------------------------------------- +143: [23:38:15] Testing UFF builder+minimization. +141: [23:38:15] done +141: [23:38:15] ------------------------------------- +141: [23:38:15] Testing Issue239. 142: processing 142: launch :0 142: launch :1 @@ -26381,48 +26423,70 @@ 142: launch :21 142: launch :22 142: launch :23 -126: Warning: Atom Count for residue GLU150A does not match expected count -141: [03:09:45] done -141: [03:09:45] ------------------------------------- -141: [03:09:45] Testing github 308: crash during MMFF parameterization . -141: [03:09:45] ------------------------------------- -141: [03:09:45] Testing SFIssue1653802. -141: [03:09:45] done -141: [03:09:45] ------------------------------------- -141: [03:09:45] Testing SFIssue2378119. -141: [03:09:45] done -141: [03:09:45] ------------------------------------- -141: [03:09:45] Test MMFF force-field parameter getters. -141: [03:09:45] ------------------------------------- -141: [03:09:45] Test MMFF multithreading +141: [23:38:15] done +141: [23:38:15] ------------------------------------- +141: [23:38:15] Testing calcEnergy with passed coords. +141: [23:38:15] done +141: [23:38:15] ------------------------------------- +141: [23:38:15] Testing calcGrad. +141: [23:38:15] done +141: [23:38:15] ------------------------------------- +141: [23:38:15] Testing Issue242. +143: [23:38:15] done +143: [23:38:15] ------------------------------------- +143: [23:38:15] Testing UFF special cases. +143: [23:38:15] UFFTYPER: Unrecognized charge state for atom: 0 +143: [23:38:15] done +143: [23:38:15] ------------------------------------- +143: [23:38:15] Testing Issue239. +136: ....... +136: ---------------------------------------------------------------------- +136: Ran 7 tests in 0.157s +136: +136: OK +143: [23:38:15] done +143: [23:38:15] ------------------------------------- +143: [23:38:15] Testing calcEnergy with passed coords. +143: [23:38:15] done +143: [23:38:15] ------------------------------------- +143: [23:38:15] Testing calcGrad. +143: [23:38:15] done +143: [23:38:15] ------------------------------------- +143: [23:38:15] Testing SFIssue1653802. +143: [23:38:15] done +143: [23:38:15] ------------------------------------- +143: [23:38:15] Testing SFIssue2378119. +143: [23:38:15] done +143: [23:38:15] ------------------------------------- +143: [23:38:15] Test UFF force-field parameter getters. +143: [23:38:15] ------------------------------------- +143: [23:38:15] Testing handling missing parameters. +143: [23:38:15] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [23:38:15] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: [23:38:15] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [23:38:15] UFFTYPER: Unrecognized atom type: Cu+1 (0) +141: [23:38:15] done +141: [23:38:15] ------------------------------------- +141: [23:38:15] Testing github 308: crash during MMFF parameterization . +141: [23:38:15] ------------------------------------- +141: [23:38:15] Testing SFIssue1653802. +141: [23:38:15] done +141: [23:38:15] ------------------------------------- +141: [23:38:15] Testing SFIssue2378119. +141: [23:38:15] done +141: [23:38:15] ------------------------------------- +141: [23:38:15] Test MMFF force-field parameter getters. +141: [23:38:15] ------------------------------------- +141: [23:38:15] Test MMFF multithreading +143: [23:38:15] done +143: [23:38:15] ------------------------------------- +143: [23:38:15] Testing SFIssue3009337. 141: generating reference data -126: Warning: Atom Count for residue ASN157A does not match expected count -139: ........ -139: ---------------------------------------------------------------------- -139: Ran 8 tests in 0.068s -139: -139: OK -131/236 Test #139: pyMolTransforms ........................ Passed 0.73 sec -test 143 - Start 143: testUFFForceFieldHelpers - -143: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers -143: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF -143: Test timeout computed to be: 1500 -142: done -142: [03:09:46] done -143: [03:09:46] ------------------------------------- -143: [03:09:46] Test UFF atom labels. -143: [03:09:46] done -143: [03:09:46] ------------------------------------- -143: [03:09:46] Test UFF atom typer. -143: [03:09:46] done -143: [03:09:46] ------------------------------------- -143: [03:09:46] Testing UFF builder tools. -143: [03:09:46] done -143: [03:09:46] ------------------------------------- -143: [03:09:46] Testing UFF builder+minimization. -132/236 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.47 sec +143: [23:38:15] done +143: [23:38:15] ------------------------------------- +143: [23:38:15] Test UFF multithreading +143: generating reference data +132/236 Test #136: pyPartialCharges ....................... Passed 0.83 sec test 144 Start 144: testCrystalForceField @@ -26431,742 +26495,626 @@ 144: Test timeout computed to be: 1500 144: ------------------------------------- 144: Test CrystalFF torsional term. -143: [03:09:46] done -143: [03:09:46] ------------------------------------- -143: [03:09:46] Testing UFF special cases. -143: [03:09:46] UFFTYPER: Unrecognized charge state for atom: 0 -143: [03:09:46] done -143: [03:09:46] ------------------------------------- -143: [03:09:46] Testing Issue239. -143: [03:09:46] done -143: [03:09:46] ------------------------------------- -143: [03:09:46] Testing calcEnergy with passed coords. -143: [03:09:46] done -143: [03:09:46] ------------------------------------- -143: [03:09:46] Testing calcGrad. -133/236 Test #144: testCrystalForceField .................. Passed 0.19 sec +126: Warning: Atom Count for residue GLU150A does not match expected count +142: done +142: [23:38:15] done +126: Warning: Atom Count for residue ASN157A does not match expected count +133/236 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.60 sec test 145 Start 145: pyForceFieldHelpers 145: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 145: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 145: Test timeout computed to be: 1500 -143: [03:09:46] done -143: [03:09:46] ------------------------------------- -143: [03:09:46] Testing SFIssue1653802. -143: [03:09:46] done -143: [03:09:46] ------------------------------------- -143: [03:09:46] Testing SFIssue2378119. -143: [03:09:46] done -143: [03:09:46] ------------------------------------- -143: [03:09:46] Test UFF force-field parameter getters. -143: [03:09:46] ------------------------------------- -143: [03:09:46] Testing handling missing parameters. -143: [03:09:46] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [03:09:46] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: [03:09:46] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [03:09:46] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: [03:09:46] done -143: [03:09:46] ------------------------------------- -143: [03:09:46] Testing SFIssue3009337. -143: [03:09:46] done -143: [03:09:46] ------------------------------------- -143: [03:09:46] Test UFF multithreading -143: generating reference data -141: processing -141: launch :0 -141: launch :1 -141: launch :2 -141: launch :3 -141: [03:09:46] Rep: 0 Mol:0 -141: [03:09:46] Rep: 0 Mol:2 -141: [03:09:46] Rep: 0 Mol:1 -141: [03:09:46] Rep: 0 Mol:5 -141: [03:09:46] Rep: 0 Mol:9 -141: [03:09:46] Rep: 0 Mol:3 -141: [03:09:46] Rep: 0 Mol:4 -141: [03:09:46] Rep: 0 Mol:13 -141: [03:09:46] Rep: 0 Mol:17 -141: [03:09:46] Rep: 0 Mol:6 -141: [03:09:46] Rep: 0 Mol:10 -141: [03:09:46] Rep: 0 Mol:8 -141: [03:09:46] Rep: 0 Mol:12 -141: [03:09:46] Rep: 0 Mol:16 -141: [03:09:46] Rep: 0 Mol:7 -141: [03:09:46] Rep: 0 Mol:11 -141: [03:09:46] Rep: 0 Mol:21 -141: [03:09:46] Rep: 0 Mol:15 -141: [03:09:46] Rep: 0 Mol:20 -141: [03:09:46] Rep: 0 Mol:24 -141: [03:09:46] Rep: 0 Mol:19 -141: [03:09:46] Rep: 0 Mol:25 -141: [03:09:46] Rep: 0 Mol:23 -141: [03:09:46] Rep: 0 Mol:27 -141: [03:09:46] Rep: 0 Mol:31 -141: [03:09:46] Rep: 0 Mol:29 -141: [03:09:46] Rep: 0 Mol:28 -141: [03:09:46] Rep: 0 Mol:14 -141: [03:09:46] Rep: 0 Mol:18 -141: [03:09:46] Rep: 0 Mol:22 -141: [03:09:46] Rep: 0 Mol:26 -141: [03:09:46] Rep: 0 Mol:30 -117: =>start test GETAWAY custom -117: [03:09:46] test on : 365 molecules done -134/236 Test #117: testRDFcustom .......................... Passed 5.24 sec +134/236 Test #144: testCrystalForceField .................. Passed 0.22 sec test 146 Start 146: testDistGeomHelpers 146: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 146: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 146: Test timeout computed to be: 1500 -146: [03:09:46] ******************************************************** -146: [03:09:46] Testing DistGeomHelpers -146: [03:09:46] --------------------------------- -146: [03:09:46] test2 +146: [23:38:15] ******************************************************** +146: [23:38:15] Testing DistGeomHelpers +146: [23:38:15] --------------------------------- +146: [23:38:15] test2 146: 146: go 146: ------------------------------------- 146: -141: [03:09:46] Rep: 20 Mol:3 -141: [03:09:46] Rep: 20 Mol:7 -141: [03:09:46] Rep: 20 Mol:11 -141: [03:09:46] Rep: 20 Mol:15 -141: [03:09:46] Rep: 20 Mol:19 -141: [03:09:46] Rep: 20 Mol:23 -141: [03:09:46] Rep: 20 Mol:27 -141: [03:09:46] Rep: 20 Mol:31 -145: [03:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:46] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:46] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:46] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:46] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:46] Molecule does not have explicit Hs. Consider calling AddHs() -145: ..[03:09:46] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:09:46] Rep: 20 Mol:1 -141: [03:09:46] Rep: 20 Mol:5 -141: [03:09:46] Rep: 20 Mol:9 -141: [03:09:46] Rep: 20 Mol:13 -141: [03:09:46] Rep: 20 Mol:17 -141: [03:09:46] Rep: 20 Mol:21 -141: [03:09:46] Rep: 20 Mol:25 -145: [03:09:46] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[03:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:46] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:09:46] Rep: 20 Mol:0 -141: [03:09:46] Rep: 20 Mol:4 -141: [03:09:46] Rep: 20 Mol:29 143: processing 143: launch :0 143: launch :1 143: launch :2 143: launch :3 -141: [03:09:46] Rep: 20 Mol:8 -141: [03:09:46] Rep: 20 Mol:12 -141: [03:09:46] Rep: 20 Mol:16 -141: [03:09:46] Rep: 20 Mol:20 -141: [03:09:46] Rep: 20 Mol:24 -145: .[03:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:46] Molecule does not have explicit Hs. Consider calling AddHs() -143: [03:09:46] Rep: 0 Mol:3 -141: [03:09:46] Rep: 20 Mol:28 -143: [03:09:46] Rep: [03:09:46] Rep: 0 Mol:2 -143: [03:09:46] Rep: 0 Mol:0 -143: [03:09:46] Rep: 0 Mol:4 -143: 0 Mol:1 -143: [03:09:46] Rep: 0 Mol:5 -143: [03:09:46] Rep: 0 Mol:9 -143: [03:09:46] Rep: 0 Mol:13 -143: [03:09:46] Rep: 0 Mol:6 -143: [03:09:46] Rep: 0 Mol:17 -143: [03:09:46] Rep: 0 Mol:10 -143: [03:09:46] Rep: 0 Mol:8 -143: [03:09:46] Rep: 0 Mol:12 -143: [03:09:46] Rep: 0 Mol:16 -143: [03:09:46] Rep: 0 Mol:7 -143: [03:09:46] Rep: 0 Mol:11 -143: [03:09:46] Rep: 0 Mol:15 -145: .[03:09:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -143: [03:09:47] Rep: 0 Mol:21 -143: [03:09:47] Rep: 0 Mol:20 -143: [03:09:47] Rep: 0 Mol:25 -143: [03:09:47] Rep: 0 Mol:19 -143: [03:09:47] Rep: 0 Mol:23 -143: [03:09:47] Rep: 0 Mol:27 -143: [03:09:47] Rep: 0 Mol:29 -145: .[03:09:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -143: [03:09:47] Rep: 0 Mol:24 -143: [03:09:47] Rep: 0 Mol:28 -143: [03:09:47] Rep: 0 Mol:14 -143: [03:09:47] Rep: 0 Mol:31 -143: [03:09:47] Rep: 0 Mol:18 -145: .[03:09:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[03:09:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [03:09:47] Rep: 0 Mol:22 -145: [03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[03:09:47] UFFTYPER: Unrecognized hybridization for atom: 0 -145: [03:09:47] UFFTYPER: Unrecognized atom type: Cu+1 (0) -145: .[03:09:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:09:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:09:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:09:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:09:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[03:09:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[03:09:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:09:47] Rep: 20 Mol:2 -141: [03:09:47] Rep: 20 Mol:6 -143: [03:09:47] Rep: 0 Mol:26 -141: [03:09:47] Rep: 20 Mol:10 -141: [03:09:47] Rep: 20 Mol:14 -141: [03:09:47] Rep: 20 Mol:18 -141: [03:09:47] Rep: 20 Mol:22 -141: [03:09:47] Rep: 20 Mol:26 -141: [03:09:47] Rep: 20 Mol:30 -145: ...[03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -143: [03:09:47] Rep: 0 Mol:30 -141: [03:09:47] Rep: 40 Mol:3 -141: [03:09:47] Rep: 40 Mol:7 -141: [03:09:47] Rep: 40 Mol:11 -141: [03:09:47] Rep: 40 Mol:15 -141: [03:09:47] Rep: 40 Mol:19 -141: [03:09:47] Rep: 40 Mol:23 -141: [03:09:47] Rep: 40 Mol:27 -141: [03:09:47] Rep: 40 Mol:31 -145: [03:09:47] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:09:47] Rep: 40 Mol:1 -141: [03:09:47] Rep: 40 Mol:5 -141: [03:09:47] Rep: 40 Mol:9 -141: [03:09:47] Rep: 40 Mol:13 -141: [03:09:47] Rep: 40 Mol:17 -141: [03:09:47] Rep: 40 Mol:21 -141: [03:09:47] Rep: 40 Mol:25 -141: [03:09:47] Rep: 40 Mol:29 -141: [03:09:47] Rep: 40 Mol:0 -141: [03:09:47] Rep: 40 Mol:4 -141: [03:09:47] Rep: 40 Mol:8 -141: [03:09:47] Rep: 40 Mol:12 -141: [03:09:47] Rep: 40 Mol:16 -141: [03:09:47] Rep: 40 Mol:20 -141: [03:09:47] Rep: 40 Mol:24 -141: [03:09:47] Rep: 40 Mol:28 +143: [23:38:15] Rep: 0 Mol:1 +143: [23:38:15] Rep: 0 Mol:5 +143: [23:38:15] Rep: 0 Mol:9 +143: [23:38:15] Rep: 0 Mol:3 +143: [23:38:15] Rep: 0 Mol:2 +143: [23:38:15] Rep: 0 Mol:0 +143: [23:38:15] Rep: 0 Mol:13 +143: [23:38:15] Rep: 0 Mol:17 +143: [23:38:15] Rep: 0 Mol:4 +143: [23:38:15] Rep: 0 Mol:7 +143: [23:38:15] Rep: 0 Mol:11 +143: [23:38:15] Rep: 0 Mol:15 +143: [23:38:15] Rep: 0 Mol:6 +143: [23:38:15] Rep: 0 Mol:10 +143: [23:38:15] Rep: 0 Mol:21 +143: [23:38:15] Rep: 0 Mol:19 +143: [23:38:15] Rep: 0 Mol:25 +143: [23:38:15] Rep: 0 Mol:23 +143: [23:38:15] Rep: 0 Mol:27 +143: [23:38:15] Rep: 0 Mol:29 +143: [23:38:15] Rep: 0 Mol:31 +143: [23:38:15] Rep: 0 Mol:8 +143: [23:38:15] Rep: 0 Mol:12 +143: [23:38:15] Rep: 0 Mol:16 +143: [23:38:15] Rep: 0 Mol:14 +143: [23:38:15] Rep: 0 Mol:20 +143: [23:38:15] Rep: 0 Mol:18 +143: [23:38:15] Rep: 0 Mol:24 +143: [23:38:15] Rep: 0 Mol:22 +143: [23:38:15] Rep: 0 Mol:28 +143: [23:38:15] Rep: 0 Mol:26 +143: [23:38:15] Rep: 0 Mol:30 +141: processing +141: launch :0 +141: launch :1 +141: launch :2 +141: launch :3 +141: [23:38:16] Rep: 0 Mol:1 +141: [23:38:16] Rep: 0 Mol:0 +141: [23:38:16] Rep: 0 Mol:5 +141: [23:38:16] Rep: 0 Mol:9 +141: [23:38:16] Rep: 0 Mol:3 +141: [23:38:16] Rep: 0 Mol:2 +141: [23:38:16] Rep: 0 Mol:4 +141: [23:38:16] Rep: 0 Mol:13 +141: [23:38:16] Rep: 0 Mol:17 +141: [23:38:16] Rep: 0 Mol:8 +141: [23:38:16] Rep: 0 Mol:6 +141: [23:38:16] Rep: 0 Mol:10 +141: [23:38:16] Rep: 0 Mol:12 +141: [23:38:16] Rep: 0 Mol:16 +141: [23:38:16] Rep: 0 Mol:21 +141: [23:38:16] Rep: 0 Mol:7 +141: [23:38:16] Rep: 0 Mol:25 +141: [23:38:16] Rep: 0 Mol:11 +141: [23:38:16] Rep: 0 Mol:20 +141: [23:38:16] Rep: 0 Mol:15 +141: [23:38:16] Rep: 0 Mol:24 +141: [23:38:16] Rep: 0 Mol:29 +141: [23:38:16] Rep: 0 Mol:19 +141: [23:38:16] Rep: 0 Mol:23 +141: [23:38:16] Rep: 0 Mol:27 +141: [23:38:16] Rep: 0 Mol:28 +141: [23:38:16] Rep: 0 Mol:31 +145: [23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: ..[23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +141: [23:38:16] Rep: 0 Mol:14 +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +141: [23:38:16] Rep: 0 Mol:18 +145: .[23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +141: [23:38:16] Rep: 0 Mol:22 +141: [23:38:16] Rep: 0 Mol:26 +145: .[23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +141: [23:38:16] Rep: 0 Mol:30 +145: .[23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[23:38:16] UFFTYPER: Unrecognized hybridization for atom: 0 +145: [23:38:16] UFFTYPER: Unrecognized atom type: Cu+1 (0) +145: .[23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[23:38:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: ...[23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:38:16] Rep: 100 Mol:1 +143: [23:38:16] Rep: 100 Mol:5 +143: [23:38:16] Rep: 100 Mol:9 +143: [23:38:16] Rep: 100 Mol:13 +143: [23:38:16] Rep: 100 Mol:17 +143: [23:38:16] Rep: 100 Mol:21 +143: [23:38:16] Rep: 100 Mol:25 +143: [23:38:16] Rep: 100 Mol:29 +145: [23:38:16] Molecule does not have explicit Hs. Consider calling AddHs() 145: ... 145: ---------------------------------------------------------------------- -145: Ran 19 tests in 0.331s +145: Ran 19 tests in 0.227s 145: 145: OK -141: [03:09:47] Rep: 60 Mol:3 -141: [03:09:47] Rep: 60 Mol:7 -141: [03:09:47] Rep: 60 Mol:11 -141: [03:09:47] Rep: 60 Mol:15 -141: [03:09:47] Rep: 60 Mol:19 -141: [03:09:47] Rep: 60 Mol:23 -141: [03:09:47] Rep: 60 Mol:27 -141: [03:09:47] Rep: 60 Mol:31 -141: [03:09:47] Rep: 40 Mol:2 -141: [03:09:47] Rep: 40 Mol:6 -141: [03:09:47] Rep: 40 Mol:10 -141: [03:09:47] Rep: 40 Mol:14 -141: [03:09:47] Rep: 40 Mol:18 -141: [03:09:47] Rep: 40 Mol:22 -141: [03:09:47] Rep: 40 Mol:26 -141: [03:09:47] Rep: 40 Mol:30 -135/236 Test #145: pyForceFieldHelpers .................... Passed 0.97 sec +143: [23:38:16] Rep: 100 Mol:3 +143: [23:38:16] Rep: 100 Mol:7 +143: [23:38:16] Rep: 100 Mol:11 +143: [23:38:16] Rep: 100 Mol:15 +143: [23:38:16] Rep: 100 Mol:19 +143: [23:38:16] Rep: 100 Mol:23 +143: [23:38:16] Rep: 100 Mol:27 +143: [23:38:16] Rep: 100 Mol:31 +141: [23:38:16] Rep: 20 Mol:1 +141: [23:38:16] Rep: 20 Mol:5 +141: [23:38:16] Rep: 20 Mol:9 +141: [23:38:16] Rep: 20 Mol:13 +141: [23:38:16] Rep: 20 Mol:17 +141: [23:38:16] Rep: 20 Mol:21 +141: [23:38:16] Rep: 20 Mol:3 +141: [23:38:16] Rep: 20 Mol:7 +141: [23:38:16] Rep: 20 Mol:25 +141: [23:38:16] Rep: 20 Mol:29 +141: [23:38:16] Rep: 20 Mol:11 +141: [23:38:16] Rep: 20 Mol:15 +141: [23:38:16] Rep: 20 Mol:0 +141: [23:38:16] Rep: 20 Mol:4 +141: [23:38:16] Rep: 20 Mol:19 +141: [23:38:16] Rep: 20 Mol:8 +141: [23:38:16] Rep: 20 Mol:23 +141: [23:38:16] Rep: 20 Mol:27 +141: [23:38:16] Rep: 20 Mol:12 +141: [23:38:16] Rep: 20 Mol:31 +141: [23:38:16] Rep: 20 Mol:16 +141: [23:38:16] Rep: 20 Mol:20 +141: [23:38:16] Rep: 20 Mol:24 +141: [23:38:16] Rep: 20 Mol:28 +135/236 Test #145: pyForceFieldHelpers .................... Passed 0.92 sec test 147 Start 147: distGeomHelpersCatch 147: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 147: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 147: Test timeout computed to be: 1500 -147: Randomness seeded to: 324715057 -141: [03:09:47] Rep: 60 Mol:0 -141: [03:09:47] Rep: 60 Mol:4 -141: [03:09:47] Rep: 60 Mol:8 -141: [03:09:47] Rep: 60 Mol:12 -141: [03:09:47] Rep: 60 Mol:16 -141: [03:09:47] Rep: 60 Mol:20 -141: [03:09:47] Rep: 60 Mol:24 -141: [03:09:47] Rep: 60 Mol:28 -141: [03:09:47] Rep: 60 Mol:1 -141: [03:09:47] Rep: 60 Mol:5 -141: [03:09:47] Rep: 60 Mol:9 -141: [03:09:47] Rep: 60 Mol:13 -141: [03:09:47] Rep: 60 Mol:17 -147: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [*: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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [$([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: [03:09:47] [$(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: [03:09:47] [$(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: [03:09:47] [$(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: [03:09:47] [$(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: [03:09:47] [$(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: [03:09:47] [$(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: [03:09:47] [$(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: [03:09:47] [$(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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] 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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: Randomness seeded to: 2586449517 +141: [23:38:16] Rep: 20 Mol:2 +141: [23:38:16] Rep: 20 Mol:6 +141: [23:38:16] Rep: 20 Mol:10 +141: [23:38:16] Rep: 20 Mol:14 +141: [23:38:16] Rep: 20 Mol:18 +147: [23:38:16] [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: [23:38:16] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] +141: [23:38:16] Rep: 20 Mol:22 +141: [23:38:16] Rep: 20 Mol:26 +141: [23:38:16] Rep: 20 Mol:30 +147: [23:38:16] [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: [23:38:16] [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: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [*: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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [$([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: [23:38:16] [$(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: [23:38:16] [$(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: [23:38:16] [$(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: [23:38:16] [$(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: [23:38:16] [$(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: [23:38:16] [$(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: [23:38:16] [$(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: [23:38:16] [$(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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] 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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [$([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: [03:09:47] [$([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: [03:09:47] [$(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: [03:09:47] [$(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)] -141: [03:09:47] Rep: 60 Mol:21 -141: [03:09:47] Rep: 60 Mol:25 -141: [03:09:47] Rep: 60 Mol:29 -147: [03:09:47] [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: [03:09:47] [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: [03:09:47] 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: [03:09:47] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -147: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [!#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: [03:09:47] [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: [03:09:47] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [$([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: [23:38:16] [$([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: [23:38:16] [$(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: [23:38:16] [$(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: [23:38:16] [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: [23:38:16] [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: [23:38:16] 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: [23:38:16] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +147: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [!#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: [23:38:16] [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: [23:38:16] [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: [03:09:47] [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: [03:09:47] [$([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: [03:09:47] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -141: [03:09:47] Rep: 80 Mol:3 -141: [03:09:47] Rep: 80 Mol:7 -147: [03:09:47] 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: [23:38:16] [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: [23:38:16] [$([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: [23:38:16] [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: [23:38:16] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 147: ----------- -141: [03:09:47] Rep: 80 Mol:11 -141: [03:09:47] Rep: 80 Mol:15 -141: [03:09:47] Rep: 80 Mol:19 -141: [03:09:47] Rep: 80 Mol:23 -141: [03:09:47] Rep: 80 Mol:27 -141: [03:09:47] Rep: 80 Mol:31 147: ----------- -147: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [$(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: [03:09:47] [$(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: [03:09:47] [$(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: [03:09:47] [$(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: [03:09:47] [$(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: [03:09:47] [$(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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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: [03:09:47] [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)] -143: [03:09:47] Rep: 100 Mol:3 -143: [03:09:47] Rep: 100 Mol:7 -143: [03:09:47] Rep: 100 Mol:11 -143: [03:09:47] Rep: 100 Mol:15 -143: [03:09:47] Rep: 100 Mol:19 -143: [03:09:47] Rep: 100 Mol:23 -143: [03:09:47] Rep: 100 Mol:27 -143: [03:09:47] Rep: 100 Mol:31 -147: [03:09:47] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -147: [03:09:47] UFFTYPER: Unrecognized charge state for atom: 1 -147: [03:09:47] UFFTYPER: Unrecognized charge state for atom: 1 -147: [03:09:47] UFFTYPER: Unrecognized charge state for atom: 1 -147: [03:09:47] UFFTYPER: Unrecognized charge state for atom: 5 -147: [03:09:47] UFFTYPER: Unrecognized charge state for atom: 5 -147: [03:09:47] UFFTYPER: Unrecognized charge state for atom: 5 -141: [03:09:47] Rep: 80 Mol:0 -141: [03:09:47] Rep: 80 Mol:4 -141: [03:09:47] Rep: 80 Mol:8 -141: [03:09:47] Rep: 80 Mol:12 -141: [03:09:47] Rep: 80 Mol:16 -141: [03:09:47] Rep: 80 Mol:20 -141: [03:09:47] Rep: 80 Mol:24 -141: [03:09:47] Rep: 80 Mol:28 -147: [03:09:47] UFFTYPER: Unrecognized charge state for atom: 6 -143: [03:09:47] Rep: 100 Mol:0 -143: [03:09:47] Rep: 100 Mol:4 -143: [03:09:47] Rep: 100 Mol:8 -143: [03:09:47] Rep: 100 Mol:12 -143: [03:09:47] Rep: 100 Mol:16 -143: [03:09:47] Rep: 100 Mol:20 -143: [03:09:47] Rep: 100 Mol:24 -143: [03:09:47] Rep: 100 Mol:28 -147: [03:09:47] UFFTYPER: Unrecognized charge state for atom: 6 -141: [03:09:47] Rep: 80 Mol:1 -141: [03:09:47] Rep: 80 Mol:5 -141: [03:09:47] Rep: 80 Mol:9 -141: [03:09:47] Rep: 80 Mol:13 -141: [03:09:47] Rep: 80 Mol:17 -141: [03:09:47] Rep: 80 Mol:21 -141: [03:09:47] Rep: 80 Mol:25 -141: [03:09:47] Rep: 80 Mol:29 -147: [03:09:47] UFFTYPER: Unrecognized charge state for atom: 6 -143: [03:09:47] Rep: 100 Mol:1 -143: [03:09:47] Rep: 100 Mol:5 -143: [03:09:47] Rep: 100 Mol:9 -143: [03:09:47] Rep: 100 Mol:13 -143: [03:09:47] Rep: 100 Mol:17 -143: [03:09:47] Rep: 100 Mol:21 -143: [03:09:47] Rep: 100 Mol:25 -143: [03:09:47] Rep: 100 Mol:29 -141: [03:09:47] Rep: 60 Mol:2 -141: [03:09:47] Rep: 60 Mol:6 -141: [03:09:47] Rep: 60 Mol:10 -141: [03:09:47] Rep: 60 Mol:14 -141: [03:09:47] Rep: 60 Mol:18 -141: [03:09:47] Rep: 60 Mol:22 -141: [03:09:47] Rep: 60 Mol:26 -141: [03:09:47] Rep: 60 Mol:30 -141: [03:09:47] Rep: 80 Mol:2 -141: [03:09:47] Rep: 80 Mol:6 -141: [03:09:47] Rep: 80 Mol:10 -141: [03:09:47] Rep: 80 Mol:14 -141: [03:09:47] Rep: 80 Mol:18 -141: [03:09:47] Rep: 80 Mol:22 -141: [03:09:47] Rep: 80 Mol:26 -141: [03:09:47] Rep: 80 Mol:30 -143: [03:09:48] Rep: 100 Mol:2 -143: [03:09:48] Rep: 100 Mol:6 -143: [03:09:48] Rep: 100 Mol:10 -143: [03:09:48] Rep: 100 Mol:14 -143: [03:09:48] Rep: 100 Mol:18 -143: [03:09:48] Rep: 100 Mol:22 -143: [03:09:48] Rep: 100 Mol:26 -143: [03:09:48] Rep: 100 Mol:30 -128: [03:09:48] done -128: [03:09:48] ------------------------------------- -128: [03:09:48] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -128: [03:09:48] done -128: [03:09:48] ------------------------------------- -128: [03:09:48] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -128: [03:09:48] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:48] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] done -128: [03:09:48] ------------------------------------- -128: [03:09:48] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -128: [03:09:48] done -128: [03:09:48] ------------------------------------- -128: [03:09:48] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] done -128: [03:09:48] ------------------------------------- -128: [03:09:48] Test unfolded version of RDKFP -128: [03:09:48] ------------------------------------- -128: [03:09:48] Test bitinfo of RDKFP -128: 562: [ 2 ], -128: 709: [ 0 1 ], -128: 1118: [ 0 1 2 ], -128: 1183: [ 1 2 ], -128: 1233: [ 0 1 2 ], -128: 1308: [ 0 ], [ 1 ], -128: 1339: [ 2 ], -128: 1728: [ 1 2 ], -128: 1772: [ 0 ], [ 1 ], -128: 1813: [ 0 1 ], -128: ------------ -128: [03:09:48] ------------------------------------- -128: [03:09:48] Single atoms setting radius 1 bits in Morgan fingerprints -128: [03:09:48] done -128: [03:09:48] ------------------------------------- -128: [03:09:48] Github #879: Pattern fingerprint should set bits for single-atom fragments. -128: [03:09:48] done -128: [03:09:48] ------------------------------------- -128: [03:09:48] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -128: [03:09:48] done -128: [03:09:48] ------------------------------------- -128: [03:09:48] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -128: [03:09:48] done -128: [03:09:48] ------------------------------------- -128: [03:09:48] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -128: [03:09:48] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:48] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:48] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:48] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:48] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:48] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:48] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:48] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:48] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:48] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:48] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:48] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:09:48] done -128: [03:09:48] ------------------------------------- -128: [03:09:48] Github #2115: BitInfo not complete for RDKFingerprint -128: [03:09:48] done -128: [03:09:48] ------------------------------------- -128: [03:09:48] Github #3723: Fingerprint crash for mols with Zero order bonds -128: [03:09:48] done -141: [03:09:48] done -141: [03:09:48] ------------------------------------- -141: [03:09:48] Test MMFF multithreading2 -136/236 Test #128: testFingerprints ....................... Passed 4.98 sec +147: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [$(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: [23:38:16] [$(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: [23:38:16] [$(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: [23:38:16] [$(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: [23:38:16] [$(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: [23:38:16] [$(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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] [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: [23:38:16] Rep: 40 Mol:3 +141: [23:38:16] Rep: 40 Mol:1 +141: [23:38:16] Rep: 40 Mol:7 +141: [23:38:16] Rep: 40 Mol:11 +141: [23:38:16] Rep: 40 Mol:15 +141: [23:38:16] Rep: 40 Mol:19 +141: [23:38:16] Rep: 40 Mol:23 +141: [23:38:16] Rep: 40 Mol:27 +141: [23:38:16] Rep: 40 Mol:31 +141: [23:38:16] Rep: 40 Mol:5 +141: [23:38:16] Rep: 40 Mol:9 +141: [23:38:16] Rep: 40 Mol:13 +141: [23:38:16] Rep: 40 Mol:17 +141: [23:38:16] Rep: 40 Mol:21 +141: [23:38:16] Rep: 40 Mol:25 +141: [23:38:16] Rep: 40 Mol:29 +143: [23:38:16] Rep: 100 Mol:0 +143: [23:38:16] Rep: 100 Mol:4 +143: [23:38:16] Rep: 100 Mol:8 +143: [23:38:16] Rep: 100 Mol:12 +143: [23:38:16] Rep: 100 Mol:16 +143: [23:38:16] Rep: 100 Mol:20 +143: [23:38:16] Rep: 100 Mol:24 +143: [23:38:16] Rep: 100 Mol:28 +141: [23:38:16] Rep: 40 Mol:0 +141: [23:38:16] Rep: 40 Mol:4 +141: [23:38:16] Rep: 40 Mol:8 +141: [23:38:16] Rep: 40 Mol:12 +141: [23:38:16] Rep: 40 Mol:16 +141: [23:38:16] Rep: 40 Mol:20 +141: [23:38:16] Rep: 40 Mol:24 +141: [23:38:16] Rep: 40 Mol:28 +147: [23:38:16] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +147: [23:38:16] UFFTYPER: Unrecognized charge state for atom: 1 +147: [23:38:16] UFFTYPER: Unrecognized charge state for atom: 1 +147: [23:38:16] UFFTYPER: Unrecognized charge state for atom: 1 +143: [23:38:16] Rep: 100 Mol:2 +143: [23:38:16] Rep: 100 Mol:6 +143: [23:38:16] Rep: 100 Mol:10 +143: [23:38:16] Rep: 100 Mol:14 +143: [23:38:16] Rep: 100 Mol:18 +143: [23:38:16] Rep: 100 Mol:22 +143: [23:38:16] Rep: 100 Mol:26 +143: [23:38:16] Rep: 100 Mol:30 +147: [23:38:16] UFFTYPER: Unrecognized charge state for atom: 5 +147: [23:38:16] UFFTYPER: Unrecognized charge state for atom: 5 +147: [23:38:16] UFFTYPER: Unrecognized charge state for atom: 5 +141: [23:38:16] Rep: 60 Mol:3 +141: [23:38:16] Rep: 60 Mol:7 +141: [23:38:16] Rep: 60 Mol:11 +141: [23:38:16] Rep: 60 Mol:15 +141: [23:38:16] Rep: 60 Mol:19 +141: [23:38:16] Rep: 60 Mol:23 +141: [23:38:16] Rep: 60 Mol:27 +141: [23:38:16] Rep: 60 Mol:31 +141: [23:38:16] Rep: 60 Mol:1 +141: [23:38:16] Rep: 60 Mol:5 +141: [23:38:16] Rep: 60 Mol:9 +141: [23:38:16] Rep: 60 Mol:13 +141: [23:38:16] Rep: 60 Mol:0 +141: [23:38:16] Rep: 60 Mol:4 +141: [23:38:16] Rep: 60 Mol:8 +141: [23:38:16] Rep: 60 Mol:12 +141: [23:38:16] Rep: 60 Mol:16 +141: [23:38:16] Rep: 60 Mol:20 +141: [23:38:16] Rep: 60 Mol:24 +141: [23:38:16] Rep: 60 Mol:28 +141: [23:38:16] Rep: 60 Mol:17 +141: [23:38:16] Rep: 60 Mol:21 +141: [23:38:16] Rep: 60 Mol:25 +141: [23:38:16] Rep: 60 Mol:29 +141: [23:38:16] Rep: 40 Mol:2 +141: [23:38:16] Rep: 40 Mol:6 +141: [23:38:16] Rep: 40 Mol:10 +141: [23:38:16] Rep: 40 Mol:14 +141: [23:38:16] Rep: 40 Mol:18 +141: [23:38:16] Rep: 40 Mol:22 +141: [23:38:16] Rep: 40 Mol:26 +141: [23:38:16] Rep: 40 Mol:30 +147: [23:38:17] UFFTYPER: Unrecognized charge state for atom: 6 +147: [23:38:17] UFFTYPER: Unrecognized charge state for atom: 6 +147: [23:38:17] UFFTYPER: Unrecognized charge state for atom: 6 +141: [23:38:17] Rep: 80 Mol:3 +141: [23:38:17] Rep: 80 Mol:7 +141: [23:38:17] Rep: 80 Mol:11 +141: [23:38:17] Rep: 80 Mol:15 +141: [23:38:17] Rep: 80 Mol:19 +141: [23:38:17] Rep: 80 Mol:23 +141: [23:38:17] Rep: 80 Mol:27 +141: [23:38:17] Rep: 80 Mol:31 +141: [23:38:17] Rep: 80 Mol:0 +141: [23:38:17] Rep: 80 Mol:4 +141: [23:38:17] Rep: 80 Mol:8 +141: [23:38:17] Rep: 80 Mol:12 +141: [23:38:17] Rep: 80 Mol:16 +141: [23:38:17] Rep: 80 Mol:20 +141: [23:38:17] Rep: 80 Mol:24 +141: [23:38:17] Rep: 80 Mol:28 +141: [23:38:17] Rep: 80 Mol:1 +141: [23:38:17] Rep: 80 Mol:5 +141: [23:38:17] Rep: 80 Mol:9 +141: [23:38:17] Rep: 80 Mol:13 +141: [23:38:17] Rep: 80 Mol:17 +141: [23:38:17] Rep: 80 Mol:21 +141: [23:38:17] Rep: 80 Mol:25 +141: [23:38:17] Rep: 80 Mol:29 +141: [23:38:17] Rep: 60 Mol:2 +141: [23:38:17] Rep: 60 Mol:6 +141: [23:38:17] Rep: 60 Mol:10 +141: [23:38:17] Rep: 60 Mol:14 +141: [23:38:17] Rep: 60 Mol:18 +141: [23:38:17] Rep: 60 Mol:22 +141: [23:38:17] Rep: 60 Mol:26 +141: [23:38:17] Rep: 60 Mol:30 +141: [23:38:17] Rep: 80 Mol:2 +141: [23:38:17] Rep: 80 Mol:6 +141: [23:38:17] Rep: 80 Mol:10 +141: [23:38:17] Rep: 80 Mol:14 +141: [23:38:17] Rep: 80 Mol:18 +141: [23:38:17] Rep: 80 Mol:22 +141: [23:38:17] Rep: 80 Mol:26 +141: [23:38:17] Rep: 80 Mol:30 +143: [23:38:17] done +143: [23:38:17] ------------------------------------- +143: [23:38:17] Test UFF multithreading2 +80: =============================================================================== +80: All tests passed (1596 assertions in 100 test cases) +80: +136/236 Test #80: fileParsersCatchTest ................... Passed 12.47 sec test 148 Start 148: pyDistGeomHelpers 148: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 148: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 148: Test timeout computed to be: 1500 -146: [03:09:46] --------------------------------- -146: [03:09:46] test3 +141: [23:38:17] done +141: [23:38:17] ------------------------------------- +141: [23:38:17] Test MMFF multithreading2 +128: [23:38:17] done +128: [23:38:17] ------------------------------------- +128: [23:38:17] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +128: [23:38:17] done +128: [23:38:17] ------------------------------------- +128: [23:38:17] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +128: [23:38:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] done +128: [23:38:17] ------------------------------------- +128: [23:38:17] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +128: [23:38:17] done +128: [23:38:17] ------------------------------------- +128: [23:38:17] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] done +128: [23:38:17] ------------------------------------- +128: [23:38:17] Test unfolded version of RDKFP +128: [23:38:17] ------------------------------------- +128: [23:38:17] Test bitinfo of RDKFP +128: 562: [ 2 ], +128: 709: [ 0 1 ], +128: 1118: [ 0 1 2 ], +128: 1183: [ 1 2 ], +128: 1233: [ 0 1 2 ], +146: [23:38:15] --------------------------------- +146: [23:38:15] test3 146: -146: [03:09:46] --------------------------------- -146: [03:09:46] test4 +146: [23:38:15] --------------------------------- +146: [23:38:15] test4 146: -146: [03:09:46] --------------------------------- -146: [03:09:46] test5 +146: [23:38:15] --------------------------------- +146: [23:38:15] test5 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] test6 +146: [23:38:17] --------------------------------- +146: [23:38:17] test6 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] test15Dists +146: [23:38:17] --------------------------------- +146: [23:38:17] test15Dists 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] test Issue 215 +146: [23:38:17] --------------------------------- +146: [23:38:17] test Issue 215 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] testMultipleConfs +146: [23:38:17] --------------------------------- +146: [23:38:17] testMultipleConfs 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] testMultipleConfsExpTors +146: [23:38:17] --------------------------------- +146: [23:38:17] testMultipleConfsExpTors 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] testIssue227 +146: [23:38:17] --------------------------------- +146: [23:38:17] testIssue227 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] testIssue236 +146: [23:38:17] --------------------------------- +146: [23:38:17] testIssue236 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] testOrdering +146: [23:38:17] --------------------------------- +146: [23:38:17] testOrdering 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] testIssue244 +146: [23:38:17] --------------------------------- +146: [23:38:17] testIssue244 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] testIssue251 +146: [23:38:17] --------------------------------- +146: [23:38:17] testIssue251 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] testIssue276 -146: [03:09:48] --------------------------------- -146: [03:09:48] testIssue284 +146: [23:38:17] --------------------------------- +146: [23:38:17] testIssue276 +146: [23:38:17] --------------------------------- +146: [23:38:17] testIssue284 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] testIssue285 +146: [23:38:17] --------------------------------- +146: [23:38:17] testIssue285 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] testIssue355 +146: [23:38:17] --------------------------------- +146: [23:38:17] testIssue355 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] testRandomCoords +146: [23:38:17] --------------------------------- +146: [23:38:17] testRandomCoords 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] test sf.net issue 1989539 +146: [23:38:17] --------------------------------- +146: [23:38:17] test sf.net issue 1989539 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] test sf.net issue 2091864 +146: [23:38:17] --------------------------------- +146: [23:38:17] test sf.net issue 2091864 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] test constrained embedding +146: [23:38:17] --------------------------------- +146: [23:38:17] test constrained embedding 146: -146: [03:09:48] ssd: 0.0752641 -146: [03:09:48] ssd: 0.0659363 -146: [03:09:48] --------------------------------- -146: [03:09:48] test sf.net issue 2091974 +146: [23:38:17] ssd: 0.0752641 +146: [23:38:17] ssd: 0.0659363 +128: 1308: [ 0 ], [ 1 ], +128: 1339: [ 2 ], +128: 1728: [ 1 2 ], +128: 1772: [ 0 ], [ 1 ], +128: 1813: [ 0 1 ], +128: ------------ +128: [23:38:17] ------------------------------------- +128: [23:38:17] Single atoms setting radius 1 bits in Morgan fingerprints +128: [23:38:17] done +128: [23:38:17] ------------------------------------- +128: [23:38:17] Github #879: Pattern fingerprint should set bits for single-atom fragments. +128: [23:38:17] done +128: [23:38:17] ------------------------------------- +128: [23:38:17] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +128: [23:38:17] done +128: [23:38:17] ------------------------------------- +128: [23:38:17] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +128: [23:38:17] done +128: [23:38:17] ------------------------------------- +128: [23:38:17] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +128: [23:38:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:17] DEPRECATION WARNING: please use AtomPairGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [23:38:17] done +128: [23:38:17] ------------------------------------- +128: [23:38:17] Github #2115: BitInfo not complete for RDKFingerprint +128: [23:38:17] done +128: [23:38:17] ------------------------------------- +128: [23:38:17] Github #3723: Fingerprint crash for mols with Zero order bonds +128: [23:38:17] done +137/236 Test #128: testFingerprints ....................... Passed 4.96 sec +test 149 + Start 149: testMolAlign + +149: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign +149: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign +149: Test timeout computed to be: 1500 +146: [23:38:17] --------------------------------- +146: [23:38:17] test sf.net issue 2091974 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] test sf.net issue 2835784 +146: [23:38:17] --------------------------------- +146: [23:38:17] test sf.net issue 2835784 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] test sf.net issue 3019283 +146: [23:38:17] --------------------------------- +146: [23:38:17] test sf.net issue 3019283 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] test sf.net issue 3238580 +146: [23:38:17] --------------------------------- +146: [23:38:17] test sf.net issue 3238580 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] test sf.net issue 3483968 +146: [23:38:17] --------------------------------- +146: [23:38:17] test sf.net issue 3483968 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] test github issue 55 +146: [23:38:18] --------------------------------- +146: [23:38:18] test github issue 55 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] test1 +146: [23:38:18] --------------------------------- +146: [23:38:18] test1 146: -146: [03:09:48] --------------------------------- -146: [03:09:48] test multi-threading +146: [23:38:18] --------------------------------- +146: [23:38:18] test multi-threading 146: 146: building molecules 146: generating reference data -141: [03:09:48] done -141: [03:09:48] ------------------------------------- -141: [03:09:48] Test MMFF multithreading3 -143: [03:09:48] done -143: [03:09:48] ------------------------------------- -143: [03:09:48] Test UFF multithreading2 -148: .[03:09:48] Molecule does not have explicit Hs. Consider calling AddHs() -147: [03:09:48] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -147: [03:09:49] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -147: [03:09:49] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -147: [03:09:49] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -147: [03:09:49] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -147: [03:09:49] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:09:49] done -141: [03:09:49] ------------------------------------- -141: [03:09:49] Testing github 162: Incorrect SMILES after MMFF parameterization . -141: [03:09:49] done -141: [03:09:49] ------------------------------------- -141: [03:09:49] Testing github 224: crash during MMFF parameterization . -141: [03:09:49] done -141: [03:09:49] ------------------------------------- -141: [03:09:49] Testing github6728: crash due to missing stretch-bend params. -137/236 Test #141: testMMFFForceFieldHelpers .............. Passed 4.04 sec -test 149 - Start 149: testMolAlign - -149: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign -149: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign -149: Test timeout computed to be: 1500 -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -143: [03:09:49] done -143: [03:09:49] ------------------------------------- -143: [03:09:49] Test UFF multithreading3 -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() 149: *********************************************************** 149: Testing MolAlign 149: --------------------------------- @@ -27188,144 +27136,233 @@ 149: testIssue241 149: 149: *********************************************************** -138/236 Test #149: testMolAlign ........................... Passed 0.22 sec +138/236 Test #149: testMolAlign ........................... Passed 0.34 sec test 150 Start 150: testO3AAlign 150: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 150: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 150: Test timeout computed to be: 1500 -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:49] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:50] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:50] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:50] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:50] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:50] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:50] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[03:09:50] Molecule does not have explicit Hs. Consider calling AddHs() -146: validating reference data -143: [03:09:50] done -143: [03:09:50] ------------------------------------- -143: [03:09:50] Testing GitHubIssue62. -143: [03:09:50] beta-lactam 39.6387 -143: [03:09:50] cyclopropanone 174.698 -143: [03:09:50] aziridine 337.986 -143: [03:09:50] aziridinone 115.248 -143: [03:09:50] isobutene 2.48217 -143: [03:09:50] acetone 1.91788 -143: [03:09:50] cyclopentanone 10.1648 -143: [03:09:50] cyclopropene 99.4921 -143: [03:09:50] cyclobutene 41.0156 -148: [03:09:50] Molecule does not have explicit Hs. Consider calling AddHs() -143: [03:09:50] cyclopropane 267.236 -143: [03:09:50] gamma-lactam 15.7471 -143: [03:09:50] trans-2,3-diphenylcyclopropan-1-one 203.398 -143: [03:09:50] cis-2,3-diphenylcyclopropan-1-one 206.852 -143: [03:09:50] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -143: [03:09:50] cyclopropylidencyclobutane 218.879 -80: =============================================================================== -80: All tests passed (1596 assertions in 100 test cases) -80: -139/236 Test #80: fileParsersCatchTest ................... Passed 13.84 sec +148: .[23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:38:18] done +143: [23:38:18] ------------------------------------- +143: [23:38:18] Test UFF multithreading3 +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +141: [23:38:18] done +141: [23:38:18] ------------------------------------- +141: [23:38:18] Test MMFF multithreading3 +148: .[23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +147: [23:38:18] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +147: [23:38:18] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +147: [23:38:18] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +147: [23:38:18] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: [23:38:18] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +147: [23:38:18] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:18] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:19] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:38:19] done +143: [23:38:19] ------------------------------------- +143: [23:38:19] Testing GitHubIssue62. +143: [23:38:19] beta-lactam 39.6387 +143: [23:38:19] cyclopropanone 174.698 +143: [23:38:19] aziridine 337.986 +143: [23:38:19] aziridinone 115.248 +141: [23:38:19] done +141: [23:38:19] ------------------------------------- +141: [23:38:19] Testing github 162: Incorrect SMILES after MMFF parameterization . +141: [23:38:19] done +141: [23:38:19] ------------------------------------- +141: [23:38:19] Testing github 224: crash during MMFF parameterization . +141: [23:38:19] done +141: [23:38:19] ------------------------------------- +141: [23:38:19] Testing github6728: crash due to missing stretch-bend params. +143: [23:38:19] isobutene 2.48217 +143: [23:38:19] acetone 1.91788 +143: [23:38:19] cyclopentanone 10.1648 +143: [23:38:19] cyclopropene 99.4921 +148: .[23:38:19] Molecule does not have explicit Hs. Consider calling AddHs() +139/236 Test #141: testMMFFForceFieldHelpers .............. Passed 4.19 sec test 151 Start 151: molAlignCatchTest 151: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 151: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 151: Test timeout computed to be: 1500 -143: [03:09:50] diphenylmethylidencyclobutane 79.6139 -143: [03:09:50] done -143: [03:09:50] ------------------------------------- -143: [03:09:50] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -143: [03:09:50] done -143: [03:09:50] ------------------------------------- -143: [03:09:50] Test square planar complexes -143: [03:09:50] done -143: [03:09:50] ------------------------------------- -143: [03:09:50] Test octahedral complexes -143: [03:09:50] done -140/236 Test #143: testUFFForceFieldHelpers ............... Passed 4.43 sec +143: [23:38:19] cyclobutene 41.0156 +143: [23:38:19] cyclopropane 267.236 +143: [23:38:19] gamma-lactam 15.7471 +143: [23:38:19] trans-2,3-diphenylcyclopropan-1-one 203.398 +143: [23:38:19] cis-2,3-diphenylcyclopropan-1-one 206.852 +148: [23:38:19] Molecule does not have explicit Hs. Consider calling AddHs() +143: [23:38:19] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +151: Randomness seeded to: 2924042053 +151: 43594809 +143: [23:38:19] cyclopropylidencyclobutane 218.879 +143: [23:38:19] diphenylmethylidencyclobutane 79.6139 +143: [23:38:19] done +143: [23:38:19] ------------------------------------- +143: [23:38:19] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +143: [23:38:19] done +143: [23:38:19] ------------------------------------- +143: [23:38:19] Test square planar complexes +143: [23:38:19] done +143: [23:38:19] ------------------------------------- +143: [23:38:19] Test octahedral complexes +143: [23:38:19] done +140/236 Test #143: testUFFForceFieldHelpers ............... Passed 4.25 sec test 152 Start 152: pyMolAlign 152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 152: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap 152: Test timeout computed to be: 1500 -148: [03:09:50] Molecule does not have explicit Hs. Consider calling AddHs() -151: Randomness seeded to: 3050923486 -151: 45377080 -95: 0,0 0 -95: 0,1 0 -95: 1,0 0 -95: 1,1 0 -95: 2,0 0 -95: 2,1 0 -151: 66917800 -141/236 Test #95: testEnumeration ........................ Passed 12.44 sec +151: 63303460 +148: [23:38:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:19] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:19] 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: [23:38:20] Molecule does not have explicit Hs. Consider calling AddHs() +125: =============================================================================== +125: All tests passed (515 assertions in 10 test cases) +125: +141/236 Test #125: descriptorsTestCatch ................... Passed 8.36 sec test 153 Start 153: testFeatures 153: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures 153: Test timeout computed to be: 1500 -153: [03:09:50] ------------------------------------- -153: [03:09:50] AtomType parser testing. -153: [03:09:50] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -153: [03:09:50] 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: [03:09:50] done -153: [03:09:50] ------------------------------------- -153: [03:09:50] FeatureDefinition parser testing. -153: [03:09:50] done -153: [03:09:50] ------------------------------------- -153: [03:09:50] Test pulling feat defs from a string. -153: [03:09:50] done -153: [03:09:50] ------------------------------------- -153: [03:09:50] FeatureDef functionality testing. -153: [03:09:50] done -153: [03:09:50] ------------------------------------- -153: [03:09:50] FeatureFactory testing. -153: [03:09:50] 1 -153: [03:09:50] 2 -153: [03:09:50] 3 -153: [03:09:50] 4 -153: [03:09:50] 5 -153: [03:09:50] 6 -153: [03:09:50] done -153: [03:09:50] ------------------------------------- -153: [03:09:50] Feature Location testing. -153: [03:09:50] done -153: [03:09:50] ------------------------------------- -153: [03:09:50] Test building a FeatureFactory from a file -153: [03:09:50] done -153: [03:09:50] ------------------------------------- -153: [03:09:50] Testing Issue 224. -153: [03:09:50] done -153: [03:09:50] ------------------------------------- -153: [03:09:50] Testing Issue 225. -153: [03:09:50] done -153: [03:09:50] ------------------------------------- -153: [03:09:50] Test Issue346 -153: [03:09:50] done -153: [03:09:50] ------------------------------------- -153: [03:09:50] Test Issue347 -153: [03:09:50] done -153: [03:09:50] ------------------------------------- -153: [03:09:50] Testing Issue 348. -153: [03:09:50] SMARTS Parse Error: syntax error while parsing: [C[C] -153: [03:09:50] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -153: [03:09:50] ------------------------------------- -153: [03:09:50] Testing Nested AtomType definitions. +153: [23:38:20] ------------------------------------- +153: [23:38:20] AtomType parser testing. +153: [23:38:20] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +153: [23:38:20] 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: [23:38:20] done +153: [23:38:20] ------------------------------------- +153: [23:38:20] FeatureDefinition parser testing. +153: [23:38:20] done +153: [23:38:20] ------------------------------------- +153: [23:38:20] Test pulling feat defs from a string. +153: [23:38:20] done +153: [23:38:20] ------------------------------------- +153: [23:38:20] FeatureDef functionality testing. +153: [23:38:20] done +153: [23:38:20] ------------------------------------- +153: [23:38:20] FeatureFactory testing. +153: [23:38:20] 1 +153: [23:38:20] 2 +153: [23:38:20] 3 +153: [23:38:20] 4 +153: [23:38:20] 5 +153: [23:38:20] 6 +153: [23:38:20] done +153: [23:38:20] ------------------------------------- +153: [23:38:20] Feature Location testing. +153: [23:38:20] done +153: [23:38:20] ------------------------------------- +153: [23:38:20] Test building a FeatureFactory from a file +153: [23:38:20] done +153: [23:38:20] ------------------------------------- +153: [23:38:20] Testing Issue 224. +153: [23:38:20] done +153: [23:38:20] ------------------------------------- +153: [23:38:20] Testing Issue 225. +153: [23:38:20] done +153: [23:38:20] ------------------------------------- +153: [23:38:20] Test Issue346 +153: [23:38:20] done +153: [23:38:20] ------------------------------------- +153: [23:38:20] Test Issue347 +153: [23:38:20] done +153: [23:38:20] ------------------------------------- +153: [23:38:20] Testing Issue 348. +153: [23:38:20] SMARTS Parse Error: syntax error while parsing: [C[C] +153: [23:38:20] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +153: [23:38:20] ------------------------------------- +153: [23:38:20] Testing Nested AtomType definitions. 153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -153: [03:09:50] ------------------------------------- -153: [03:09:50] Testing Github Issue #252: crash when calling getPos() with no conformer. -153: [03:09:50] expect a precondition failure message below -153: [03:09:50] +153: [23:38:20] ------------------------------------- +153: [23:38:20] Testing Github Issue #252: crash when calling getPos() with no conformer. +153: [23:38:20] expect a precondition failure message below +153: [23:38:20] 153: 153: **** 153: Pre-condition Violation @@ -27338,51 +27375,46 @@ 153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -153: 4# 0x0000AAAAD1691AB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 5# 0x0000AAAAD1684568 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 6# 0x0000FFFF9D38229C in /lib/aarch64-linux-gnu/libc.so.6 +153: 4# 0x0000AAAABA461AB0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 5# 0x0000AAAABA454568 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 6# 0x0000FFFF914A229C in /lib/aarch64-linux-gnu/libc.so.6 153: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -153: 8# 0x0000AAAAD1684730 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 8# 0x0000AAAABA454730 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: ---------- 153: **** 153: -153: [03:09:50] Done -153: [03:09:50] ------------------------------------- -153: [03:09:50] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -153: [03:09:50] done -142/236 Test #153: testFeatures ........................... Passed 0.03 sec +153: [23:38:20] Done +153: [23:38:20] ------------------------------------- +153: [23:38:20] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +153: [23:38:20] done +142/236 Test #153: testFeatures ........................... Passed 0.06 sec test 154 Start 154: pyChemicalFeatures 154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 154: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 154: Test timeout computed to be: 1500 -148: [03:09:50] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:51] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[03:09:51] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[03:09:51] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:09:51] Molecule does not have explicit Hs. Consider calling AddHs() -154: ..[03:09:51] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[03:09:51] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[03:09:51] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -154: [03:09:51] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +154: .[23:38:20] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[23:38:20] Molecule does not have explicit Hs. Consider calling AddHs() +154: ..[23:38:20] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[23:38:20] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[23:38:20] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +154: [23:38:20] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' 154: ... 154: ---------------------------------------------------------------------- -154: Ran 9 tests in 0.180s +154: Ran 9 tests in 0.127s 154: 154: OK -146: processing -146: launch :0 -146: launch :1 -146: launch :2 -146: launch :3 -143/236 Test #154: pyChemicalFeatures ..................... Passed 0.95 sec +146: validating reference data +148: [23:38:20] Molecule does not have explicit Hs. Consider calling AddHs() +143/236 Test #154: pyChemicalFeatures ..................... Passed 0.61 sec test 155 Start 155: testShapeHelpers 155: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 155: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers 155: Test timeout computed to be: 1500 +151: 1473680807 155: *********************************************************** 155: Testing ShapeHelpers 155: --------------------------------- @@ -27395,186 +27427,91 @@ 155: testGithub4364 155: 155: *********************************************************** -144/236 Test #155: testShapeHelpers ....................... Passed 0.05 sec +144/236 Test #155: testShapeHelpers ....................... Passed 0.06 sec test 156 Start 156: pyShapeHelpers 156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" 156: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 156: Test timeout computed to be: 1500 -125: Warning: Atom Count for residue GLU5A does not match expected count -125: Warning: Atom Count for residue ASN39A does not match expected count -125: Warning: Atom Count for residue GLU53A does not match expected count -125: Warning: Atom Count for residue ARG64A does not match expected count -125: Warning: Atom Count for residue LYS80A does not match expected count -126: Warning: Atom Count for residue GLU5A 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 -126: Warning: Atom Count for residue ASN39A does not match expected count -126: Warning: Atom Count for residue GLU53A does not match expected count -126: Warning: Atom Count for residue ARG64A does not match expected count -126: Warning: Atom Count for residue LYS80A does not match expected count -126: Warning: Atom Count for residue GLU150A does not match expected count -126: Warning: Atom Count for residue ASN157A does not match expected count -126: .[03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: .[03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: ..[03:09:52] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:52] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:52] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:52] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:52] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:52] DEPRECATION WARNING: please use AtomPairGenerator -126: .[03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ...[03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: [03:09:52] DEPRECATION WARNING: please use MorganGenerator -126: ....[03:09:52] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:52] DEPRECATION WARNING: please use AtomPairGenerator -126: ....[03:09:52] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:09:52] DEPRECATION WARNING: please use AtomPairGenerator -126: .[03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: .[03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:09:52] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ... -126: ---------------------------------------------------------------------- -126: Ran 31 tests in 8.596s -126: -126: OK -126: exactmw 78.046950192 -126: amw 78.11399999999999 -126: lipinskiHBA 0.0 -126: lipinskiHBD 0.0 -126: NumRotatableBonds 0.0 -126: NumHBD 0.0 -126: NumHBA 0.0 -126: NumHeavyAtoms 6.0 -126: NumAtoms 12.0 -126: NumHeteroatoms 0.0 -126: NumAmideBonds 0.0 -126: FractionCSP3 0.0 -126: NumRings 1.0 -126: NumAromaticRings 1.0 -126: NumAliphaticRings 0.0 -126: NumSaturatedRings 0.0 -126: NumHeterocycles 0.0 -126: NumAromaticHeterocycles 0.0 -126: NumSaturatedHeterocycles 0.0 -126: NumAliphaticHeterocycles 0.0 -126: NumSpiroAtoms 0.0 -126: NumBridgeheadAtoms 0.0 -126: NumAtomStereoCenters 0.0 -126: NumUnspecifiedAtomStereoCenters 0.0 -126: labuteASA 37.43140311949697 -126: tpsa 0.0 -126: CrippenClogP 1.6866 -126: CrippenMR 26.441999999999993 -126: chi0v 3.464101615137755 -126: chi1v 2.0000000000000004 -126: chi2v 0.6666666666666671 -126: chi3v 0.6666666666666671 -126: chi4v 0.38490017945975075 -126: chi0n 3.464101615137755 -126: chi1n 2.0000000000000004 -126: chi2n 0.6666666666666671 -126: chi3n 0.6666666666666671 -126: chi4n 0.38490017945975075 -126: hallKierAlpha -0.78 -126: kappa1 3.4115708812260532 -126: kappa2 1.6057694396735218 -126: kappa3 0.5823992601400448 -126: Phi 0.9130327103921437 -126: CustomNumAtoms 6.0 -126: exactmw 78.046950192 -126: lipinskiHBA 0.0 -125: =============================================================================== -125: All tests passed (515 assertions in 10 test cases) -125: -145/236 Test #125: descriptorsTestCatch ................... Passed 9.17 sec +148: [23:38:20] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:20] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:21] Molecule does not have explicit Hs. Consider calling AddHs() +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +156: . +156: ---------------------------------------------------------------------- +156: Ran 1 test in 0.051s +156: +156: OK +156: Testing Shape Helpers wrapper +148: [23:38:21] Molecule does not have explicit Hs. Consider calling AddHs() +151: 509321656 +151: =============================================================================== +151: All tests passed (73 assertions in 3 test cases) +151: +145/236 Test #151: molAlignCatchTest ...................... Passed 2.21 sec test 157 Start 157: testMolCatalog 157: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 157: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog 157: Test timeout computed to be: 1500 -148: [03:09:52] Molecule does not have explicit Hs. Consider calling AddHs() -146/236 Test #157: testMolCatalog ......................... Passed 0.05 sec +146/236 Test #156: pyShapeHelpers ......................... Passed 0.52 sec test 158 Start 158: pyMolCatalog 158: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 158: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 158: Test timeout computed to be: 1500 -156: . -156: ---------------------------------------------------------------------- -156: Ran 1 test in 0.074s -156: -156: OK -156: Testing Shape Helpers wrapper -147/236 Test #126: pyMolDescriptors ....................... Passed 9.28 sec +147/236 Test #157: testMolCatalog ......................... Passed 0.03 sec test 159 Start 159: moldraw2DTest1 159: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 159: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 159: Test timeout computed to be: 1500 -148/236 Test #156: pyShapeHelpers ......................... Passed 0.60 sec -test 160 - Start 160: moldraw2DTestCatch - -160: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D -160: Test timeout computed to be: 1500 +29: All 191 tests passed +29: done +29: ------------------------------------- +29: Unit tests for all MMFF constraint terms. +148: [23:38:21] Molecule does not have explicit Hs. Consider calling AddHs() 159: ----------------- Test 1 +29: 10.0003 159: file test1_6.svg gave hash 1109656969U not the expected 2635907956U 159: Done 159: ----------------- Test 2 -148: [03:09:52] Molecule does not have explicit Hs. Consider calling AddHs() 159: file test2_1.png gave hash 2467931916U not the expected 638584804U +29: done +29: ------------------------------------- +29: Unit test for MMFF TorsionConstraint close to 0 degrees. +29: done +29: ------------------------------------- +29: Unit tests for copying MMFF ForceFields. 159: file test2_2.png gave hash 3737953282U not the expected 610424244U 159: file test2_3.png gave hash 2294574389U not the expected 2179746375U 159: Done 159: ----------------- Test 4 +29: done +29: ------------------------------------- +29: Unit test for MMFF butane scan. 159: file test4_1.png gave hash 516573244U not the expected 3993974247U 159: Done 159: ----------------- Test 5 -160: Randomness seeded to: 78233684 -160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U -160: file contourMol_2.svg gave hash 2761342533U not the expected 1815941817U 159: file test5_1.png gave hash 2590128341U not the expected 571291290U -160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U +95: 0,0 0 +95: 0,1 0 +95: 1,0 0 +95: 1,1 0 +95: 2,0 0 +95: 2,1 0 +148/236 Test #95: testEnumeration ........................ Passed 15.15 sec +test 160 + Start 160: moldraw2DTestCatch + +160: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D +160: Test timeout computed to be: 1500 159: file test5_2.png gave hash 2869651309U not the expected 97265124U -160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U -160: file contourMol_5.svg gave hash 3376179346U not the expected 3792684719U 159: file test5_3.png gave hash 4285469383U not the expected 606188176U 159: Done 159: ----------------- Test 6 (atom labels) @@ -27588,132 +27525,227 @@ 159: ----------------- Test multi-threaded drawing 159: reading molecules 159: generating reference drawings -160: file testGithub3226_1.png gave hash 632134109U not the expected 3165135374U -160: file testGithub3226_2.png gave hash 1790248804U not the expected 643975155U -160: file testGithub3226_3.png gave hash 1296655029U not the expected 3119571946U -160: file testPNGMetadata_1.png gave hash 2053548476U not the expected 997629701U -160: file testPNGMetadata_2.png gave hash 1147517534U not the expected 1797853056U -159: processing -159: launch :0 -159: launch :1 -159: launch :2 -159: launch :3 -151: 1937420600 -148: [03:09:52] Molecule does not have explicit Hs. Consider calling AddHs() 158: . 158: ---------------------------------------------------------------------- -158: Ran 1 test in 0.030s +158: Ran 1 test in 0.009s 158: 158: OK -160: [03:09:52] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:09:52] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U -160: [03:09:52] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:09:52] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -160: file testHandDrawn-1.png gave hash 1854123184U not the expected 3894611804U -160: [03:09:52] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:09:52] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -149/236 Test #158: pyMolCatalog ........................... Passed 0.75 sec +160: Randomness seeded to: 1611265823 +160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U +160: file contourMol_2.svg gave hash 2761342533U not the expected 1815941817U +160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U +160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U +160: file contourMol_5.svg gave hash 3376179346U not the expected 3792684719U +149/236 Test #158: pyMolCatalog ........................... Passed 0.36 sec test 161 Start 161: moldraw2DRxnTest1 161: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 161: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 161: Test timeout computed to be: 1500 -148: [03:09:52] Molecule does not have explicit Hs. Consider calling AddHs() -160: file testHandDrawn-2.svg gave hash 700659102U not the expected 794717511U -160: [03:09:52] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:09:52] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +159: processing +159: launch :0 +159: launch :1 +159: launch :2 +159: launch :3 161: ----------------- Test 1 -160: file testHandDrawn-2.png gave hash 3861646972U not the expected 1443443188U -160: [03:09:53] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:09:53] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U -160: [03:09:53] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:09:53] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: file testGithub3226_1.png gave hash 632134109U not the expected 3165135374U +160: file testGithub3226_2.png gave hash 1790248804U not the expected 643975155U 161: file rxn_test1_1.png gave hash 2332294744U not the expected 801892091U -160: file testHandDrawn-3.png gave hash 2744546773U not the expected 865629432U +160: file testGithub3226_3.png gave hash 1296655029U not the expected 3119571946U +160: file testPNGMetadata_1.png gave hash 2053548476U not the expected 997629701U 161: file rxn_test1_2.png gave hash 3186000742U not the expected 507435337U -29: All 191 tests passed -29: done -29: ------------------------------------- -29: Unit tests for all MMFF constraint terms. -160: [03:09:53] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:09:53] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U -160: [03:09:53] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:09:53] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +148: .[23:38:21] Molecule does not have explicit Hs. Consider calling AddHs() 161: file rxn_test1_3.png gave hash 2120547110U not the expected 1590809137U +160: file testPNGMetadata_2.png gave hash 1147517534U not the expected 1797853056U 161: file rxn_test1_4.png gave hash 59268109U not the expected 1766700542U -160: file testHandDrawn-4.png gave hash 2378590163U not the expected 3919767093U 161: file rxn_test1_5.png gave hash 3733738372U not the expected 2552100594U -29: 10.0003 161: file rxn_test1_6.png gave hash 2102224395U not the expected 3791582903U 29: done -29: ------------------------------------- -29: Unit test for MMFF TorsionConstraint close to 0 degrees. -29: done -29: ------------------------------------- -29: Unit tests for copying MMFF ForceFields. +160: [23:38:21] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [23:38:21] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 161: file rxn_test1_7.png gave hash 3541821286U not the expected 1461397406U -29: done -29: ------------------------------------- -29: Unit test for MMFF butane scan. 161: Done 161: ----------------- Test 2: some examples that caused problems in testing +150/236 Test #29: testMMFFForceField ..................... Passed 18.93 sec +test 162 + Start 162: pyMolDraw2D + +162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" +162: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap +162: Test timeout computed to be: 1500 +160: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U +160: [23:38:21] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [23:38:21] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 161: file rxn_test2_1.png gave hash 2631413446U not the expected 3551633840U +160: file testHandDrawn-1.png gave hash 1854123184U not the expected 3894611804U +126: Warning: Atom Count for residue GLU5A does not match expected count 161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C -148: [03:09:53] Molecule does not have explicit Hs. Consider calling AddHs() +126: Warning: Atom Count for residue ASN39A does not match expected count +126: Warning: Atom Count for residue GLU53A does not match expected count +126: Warning: Atom Count for residue ARG64A does not match expected count +126: Warning: Atom Count for residue LYS80A does not match expected count 161: file rxn_test2_2_1.png gave hash 1629337085U not the expected 1268122583U 161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl +126: Warning: Atom Count for residue GLU150A does not match expected count +126: Warning: Atom Count for residue ASN157A does not match expected count +160: [23:38:22] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [23:38:22] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 161: file rxn_test2_2_2.png gave hash 4159784239U not the expected 82821108U 161: 2 Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C 161: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl 161: 3 [c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C +160: file testHandDrawn-2.svg gave hash 700659102U not the expected 794717511U +160: [23:38:22] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [23:38:22] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 161: file rxn_test2_2_3.png gave hash 351157945U not the expected 3828365604U 161: 3 [CH3:1]c1c(cc(n1[CH3:2])C(C)(C)C)[C:3]>>[CH3:2]c1c(c(nc(n1)[CH3:1])[C:3])OC Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3cc(n(c3C)C)C(C)(C)C Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3c(c(nc(n3)C)C)OC 161: file rxn_test2_2_4.png gave hash 3038415749U not the expected 1230108677U 161: Done 161: ----------------- Test 3: test reactant highlighting -151: 716212640 -151: =============================================================================== -151: All tests passed (73 assertions in 3 test cases) -151: -150/236 Test #151: molAlignCatchTest ...................... Passed 2.94 sec -test 162 - Start 162: pyMolDraw2D - -162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" -162: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap -162: Test timeout computed to be: 1500 +160: file testHandDrawn-2.png gave hash 3861646972U not the expected 1443443188U +160: [23:38:22] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [23:38:22] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U +160: [23:38:22] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [23:38:22] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +126: .[23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: .[23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: ..[23:38:22] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:22] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:22] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:22] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:22] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:22] DEPRECATION WARNING: please use AtomPairGenerator +126: .[23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +160: file testHandDrawn-3.png gave hash 2744546773U not the expected 865629432U +126: [23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ...[23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +126: [23:38:22] DEPRECATION WARNING: please use MorganGenerator +160: [23:38:22] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [23:38:22] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U +160: [23:38:22] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [23:38:22] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 161: file rxn_test3_1.png gave hash 3254654119U not the expected 4189980366U +126: ....[23:38:22] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:22] DEPRECATION WARNING: please use AtomPairGenerator +160: file testHandDrawn-4.png gave hash 2378590163U not the expected 3919767093U 161: Done 161: ----------------- Test 4: some examples from SMARTS in testing 161: draw! +126: ....[23:38:22] DEPRECATION WARNING: please use AtomPairGenerator +126: [23:38:22] DEPRECATION WARNING: please use AtomPairGenerator +126: .[23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [23:38:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ... +126: ---------------------------------------------------------------------- +126: Ran 31 tests in 9.566s +126: +126: OK +126: exactmw 78.046950192 +126: amw 78.11399999999999 +126: lipinskiHBA 0.0 +126: lipinskiHBD 0.0 +126: NumRotatableBonds 0.0 +126: NumHBD 0.0 +126: NumHBA 0.0 +126: NumHeavyAtoms 6.0 +126: NumAtoms 12.0 +126: NumHeteroatoms 0.0 +126: NumAmideBonds 0.0 +126: FractionCSP3 0.0 +126: NumRings 1.0 +126: NumAromaticRings 1.0 +126: NumAliphaticRings 0.0 +126: NumSaturatedRings 0.0 +126: NumHeterocycles 0.0 +126: NumAromaticHeterocycles 0.0 +126: NumSaturatedHeterocycles 0.0 +126: NumAliphaticHeterocycles 0.0 +126: NumSpiroAtoms 0.0 +126: NumBridgeheadAtoms 0.0 +126: NumAtomStereoCenters 0.0 +126: NumUnspecifiedAtomStereoCenters 0.0 +126: labuteASA 37.43140311949697 +126: tpsa 0.0 +126: CrippenClogP 1.6866 +126: CrippenMR 26.441999999999993 +126: chi0v 3.464101615137755 +126: chi1v 2.0000000000000004 +126: chi2v 0.6666666666666671 +126: chi3v 0.6666666666666671 +126: chi4v 0.38490017945975075 +126: chi0n 3.464101615137755 +126: chi1n 2.0000000000000004 +126: chi2n 0.6666666666666671 +126: chi3n 0.6666666666666671 +126: chi4n 0.38490017945975075 +126: hallKierAlpha -0.78 +126: kappa1 3.4115708812260532 +126: kappa2 1.6057694396735218 +126: kappa3 0.5823992601400448 +126: Phi 0.9130327103921437 +126: CustomNumAtoms 6.0 +126: exactmw 78.046950192 +126: lipinskiHBA 0.0 161: file rxn_test4_1.png gave hash 4262495936U not the expected 2745201873U 161: done -29: done -148: [03:09:53] Molecule does not have explicit Hs. Consider calling AddHs() -151/236 Test #29: testMMFFForceField ..................... Passed 19.44 sec +161: file rxn_test4_2.png gave hash 2281531937U not the expected 3094925886U +161: Done +151/236 Test #161: moldraw2DRxnTest1 ...................... Passed 0.54 sec test 163 Start 163: testFMCS 163: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/testFMCS 163: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS 163: Test timeout computed to be: 1500 -161: file rxn_test4_2.png gave hash 2281531937U not the expected 3094925886U -161: Done -152/236 Test #161: moldraw2DRxnTest1 ...................... Passed 0.75 sec +152/236 Test #126: pyMolDescriptors ....................... Passed 10.55 sec test 164 Start 164: pyFMCS 164: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Wrap/testFMCS.py" 164: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap 164: Test timeout computed to be: 1500 -162: ...[03:09:54] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -162: [03:09:54] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -162: ..........[03:09:54] +146: processing +146: launch :0 +146: launch :1 +146: launch :2 +146: launch :3 +162: ...[23:38:22] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +162: [23:38:22] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +162: ..........[23:38:22] 162: 162: **** 162: Pre-condition Violation @@ -27727,7 +27759,7 @@ 162: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 162: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector7 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 162: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -162: 5# 0x0000FFFF8F0A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +162: 5# 0x0000FFFFB21E2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 162: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 162: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 162: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -27738,17 +27770,17 @@ 162: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 162: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 162: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 16# 0x0000FFFF8E6BC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 17# 0x0000FFFF8E6BC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 18# 0x0000FFFF8E6BC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 19# 0x0000FFFF8E6BC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 20# 0x0000FFFF8E6BC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 16# 0x0000FFFFB17FC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 17# 0x0000FFFFB17FC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 18# 0x0000FFFFB17FC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 19# 0x0000FFFFB17FC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 20# 0x0000FFFFB17FC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 162: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 162: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 162: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 162: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 162: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -162: 26# 0x0000FFFF8F09F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +162: 26# 0x0000FFFFB21DF25C 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# 0x0000000000536550 in /usr/bin/python3 @@ -27780,19 +27812,49 @@ 162: 55# 0x0000000000628F70 in /usr/bin/python3 162: 56# Py_RunMain in /usr/bin/python3 162: 57# Py_BytesMain in /usr/bin/python3 -162: 58# 0x0000FFFF909C229C in /lib/aarch64-linux-gnu/libc.so.6 +162: 58# 0x0000FFFFB3B0229C 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: +150: *********************************************************** +150: Testing O3AAlign +150: --------------------------------- +150: testMMFFO3A +150: +150: --------------------------------- +150: testMMFFO3A with pre-computed dmat and MolHistogram +150: +150: --------------------------------- +150: testMMFFO3A with constraints +150: +150: --------------------------------- +150: testMMFFO3A with variable weight constraints followed by local-only optimization +150: +150: --------------------------------- +150: testCrippenO3A +150: +150: --------------------------------- +150: testCrippenO3A with pre-computed dmat and MolHistogram +150: +150: --------------------------------- +150: testCrippenO3A with constraints +150: +150: --------------------------------- +150: testCrippenO3A with variable weight constraints followed by local-only optimization +150: +150: --------------------------------- +150: testMMFFO3A multithreading +150: +150: generating reference data 162: ...................... 162: ---------------------------------------------------------------------- -162: Ran 35 tests in 0.414s +162: Ran 35 tests in 0.369s 162: 162: OK 162: json lasso -153/236 Test #162: pyMolDraw2D ............................ Passed 1.10 sec +153/236 Test #162: pyMolDraw2D ............................ Passed 1.28 sec test 165 Start 165: FMCStest @@ -29764,72 +29826,39 @@ 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 165: ERROR: RDKit could not load input file -154/236 Test #165: FMCStest ............................... Passed 0.13 sec +154/236 Test #165: FMCStest ............................... Passed 0.11 sec test 166 Start 166: molHashCatchTest 166: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 166: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash 166: Test timeout computed to be: 1500 -160: file testHandDrawn-5a.svg gave hash 2796249138U not the expected 1567781555U -160: [03:09:54] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:09:54] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-5b.svg gave hash 4043231252U not the expected 66354106U -160: [03:09:54] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:09:54] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -148: .[03:09:54] Molecule does not have explicit Hs. Consider calling AddHs() -166: Randomness seeded to: 2574486391 +166: Randomness seeded to: 2360577356 166: =============================================================================== 166: All tests passed (363 assertions in 14 test cases) 166: -155/236 Test #166: molHashCatchTest ....................... Passed 0.11 sec +155/236 Test #166: molHashCatchTest ....................... Passed 0.13 sec test 167 Start 167: pyMolHash 167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/Wrap/testMolHash.py" 167: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap 167: Test timeout computed to be: 1500 -150: *********************************************************** -150: Testing O3AAlign -150: --------------------------------- -150: testMMFFO3A -150: -150: --------------------------------- -150: testMMFFO3A with pre-computed dmat and MolHistogram -150: -150: --------------------------------- -150: testMMFFO3A with constraints -150: -150: --------------------------------- -150: testMMFFO3A with variable weight constraints followed by local-only optimization -150: -150: --------------------------------- -150: testCrippenO3A -150: -150: --------------------------------- -150: testCrippenO3A with pre-computed dmat and MolHistogram -150: -150: --------------------------------- -150: testCrippenO3A with constraints -150: -150: --------------------------------- -150: testCrippenO3A with variable weight constraints followed by local-only optimization -150: -150: --------------------------------- -150: testMMFFO3A multithreading -150: -150: generating reference data +160: file testHandDrawn-5a.svg gave hash 2796249138U not the expected 1567781555U +160: [23:38:23] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [23:38:23] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-5b.svg gave hash 4043231252U not the expected 66354106U +160: [23:38:23] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [23:38:23] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-5.png gave hash 2095603616U not the expected 828378555U 160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U -160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U -160: [03:09:55] unrecognized bond typefile testGithub4238_1.png gave hash 3445079665U not the expected 2623427676U -160: file testGithub4323_1.png gave hash 1102454531U not the expected 3075787867U 167: .... 167: ---------------------------------------------------------------------- -167: Ran 4 tests in 0.020s +167: Ran 4 tests in 0.024s 167: 167: OK -156/236 Test #167: pyMolHash .............................. Passed 0.65 sec +160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U +156/236 Test #167: pyMolHash .............................. Passed 0.56 sec test 168 Start 168: testMMPA @@ -29838,7 +29867,7 @@ 168: Test timeout computed to be: 1500 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.002286 seconds +168: Time elapsed 0.002291 seconds 168: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 168: 1: NOREF. Reference data NOT LISTED in test case. 168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -29879,7 +29908,7 @@ 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 0.010208 seconds +168: Time elapsed 0.001986 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 @@ -29906,6 +29935,7 @@ 168: 11: NOREF. Reference data NOT LISTED in test case.C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 12: PASSED. matchedRefRes = 8 +160: [23:38:24] unrecognized bond typefile testGithub4238_1.png gave hash 3445079665U not the expected 2623427676U 168: 13: NULL, Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 13: PASSED. matchedRefRes = 9 168: 14: C([*:1])[*:2], Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] @@ -29921,7 +29951,7 @@ 168: ----------------------------------- 168: 168: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -168: Time elapsed 0.001977 seconds +168: Time elapsed 0.002006 seconds 168: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 168: 1: PASSED. matchedRefRes = 4 168: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] @@ -29948,6 +29978,7 @@ 168: 12: PASSED. matchedRefRes = 8 168: 13: res= NULL,Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 13: PASSED. matchedRefRes = 9 +160: file testGithub4323_1.png gave hash 1102454531U not the expected 3075787867U 168: 14: res= C([*:1])[*:2],Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 14: PASSED. matchedRefRes = 11 168: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] @@ -29961,7 +29992,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -168: Time elapsed 0.000576 seconds +168: Time elapsed 0.000558 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] @@ -29983,7 +30014,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.010304 seconds +168: Time elapsed 0.010417 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 @@ -30026,7 +30057,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -168: Time elapsed 0.014573 seconds +168: Time elapsed 0.002346 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 @@ -30067,7 +30098,7 @@ 168: --- ALL PASSED --- 168: ----------------------------------- 168: 5 TEST CASES FAILED -157/236 Test #168: testMMPA ............................... Passed 0.22 sec +157/236 Test #168: testMMPA ............................... Passed 0.15 sec test 169 Start 169: pyMMPA @@ -30075,41 +30106,53 @@ 169: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap 169: Test timeout computed to be: 1500 160: file testGithub4323_3.png gave hash 2734641420U not the expected 381907253U -160: [03:09:55] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +160: [23:38:24] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +150: processing +150: launch :0 +150: launch :1 +150: launch :2 +150: launch :3 +160: file testFlexiCanvas.2a.png gave hash 1840424214U not the expected 2609920321U +160: file testFlexiCanvas.2b.png gave hash 3366044980U not the expected 3615599154U +160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U +160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U +160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U +160: file testGithub4764.sz1.png gave hash 3992785979U not the expected 2179222277U +160: file testGithub4764.sz2.png gave hash 3438062002U not the expected 444262090U 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 0.060 seconds +163: Time elapsed 0.089 seconds 163: 163: test190() 163: MCS: [#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1 19 atoms, 21 bonds -163: Time elapsed 0.005 seconds +163: Time elapsed 0.013 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 0.021 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 0.105 seconds +163: Time elapsed 0.179 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 0.103 seconds +163: Time elapsed 0.173 seconds 163: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -163: Time elapsed 0.114 seconds +163: Time elapsed 0.255 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 0.117 seconds +163: Time elapsed 0.255 seconds 163: 163: testSegFault() 163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.014 seconds +163: Time elapsed 0.029 seconds 163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.015 seconds +163: Time elapsed 0.031 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 0.011 seconds +163: Time elapsed 0.019 seconds 163: 163: testThreshold() 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds @@ -30117,11 +30160,11 @@ 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 0.365 seconds +163: Time elapsed 0.613 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 0.532 seconds +163: Time elapsed 0.540 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 0.561 seconds +163: Time elapsed 0.608 seconds 163: 163: testAtomCompareIsotopes() 163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds @@ -30147,21 +30190,32 @@ 163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds 163: Time elapsed 0.013 seconds 163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds -163: Time elapsed 0.009 seconds +160: file testGithub4764.sz3.png gave hash 850758438U not the expected 3567162200U +160: file github5383_1.svg gave hash 2761342533U not the expected 1815941817U +160: file github5383_2.svg gave hash 2560846108U not the expected 0U +160: file github5383_1.png gave hash 482266761U not the expected 2893520928U +160: file acs1996_1.png gave hash 2331419344U not the expected 2329725800U +160: file acs1996_2.png gave hash 2927836808U not the expected 2996350718U +160: file acs1996_3.svg gave hash 510450189U not the expected 879041204U +160: file acs1996_8.svg gave hash 3359655656U not the expected 4110469272U +160: file acs1996_10.svg gave hash 1008047306U not the expected 2229333301U +160: [23:38:25] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. +160: file bond_highlights_8.svg gave hash 197391689U not the expected 3119784980U +163: Time elapsed 0.001 seconds 163: 163: test18() 163: Query +MAP [CH3:0][c:1]1[n:2][c:3]([CH2:4][N:5]([CH:6]([CH3:7])[c:8]2[n:9][cH:10][cH:11][cH:12][cH:13]2)[CH2:14][CH2:15][CH2:16][CH2:17][NH2:18])[cH:19][cH:20][cH:21]1 163: MCS: [#6](:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#7]:[#6]:[#6]:[#6]:[#6]:1)-[#6]-[#6]-[#6]-[#6]-[#7]):[#6]:[#6]:[#6] 21 atoms, 21 bonds -163: Time elapsed 0.012 seconds +163: Time elapsed 0.004 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 0.074 seconds +163: Time elapsed 0.167 seconds 163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 163: Time elapsed 0.001 seconds 163: MCS: [#6]1-[#6]-[#7]-[#6](-[#6]-[#7]-1-[#6]1:[#6](:[#6]:[#6]2:[#6](:[#6](:[#6]:[#7](-[#6]3-[#6]-[#6]-3):[#6]:2:[#6]:1)-[#6](=[#8])-[#8])=[#8])-[#9])-[#6] 25 atoms, 28 bonds -163: Time elapsed 0.016 seconds +163: Time elapsed 0.047 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 0.0009 seconds. bond[0]=6 163: STATISTICS: @@ -30280,43 +30334,8 @@ 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: done -160: file testFlexiCanvas.2a.png gave hash 1840424214U not the expected 2609920321U -160: file testFlexiCanvas.2b.png gave hash 3366044980U not the expected 3615599154U -160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U -160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U -160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U -160: file testGithub4764.sz1.png gave hash 3992785979U not the expected 2179222277U -160: file testGithub4764.sz2.png gave hash 3438062002U not the expected 444262090U -160: file testGithub4764.sz3.png gave hash 850758438U not the expected 3567162200U -163: [03:09:56] The provided InitialSeed is not an MCS and will be ignored -160: file github5383_1.svg gave hash 2761342533U not the expected 1815941817U -160: file github5383_2.svg gave hash 2560846108U not the expected 0U -150: processing -150: launch :0 -150: launch :1 -150: launch :2 -150: launch :3 -160: file github5383_1.png gave hash 482266761U not the expected 2893520928U -160: file acs1996_1.png gave hash 2331419344U not the expected 2329725800U -160: file acs1996_2.png gave hash 2927836808U not the expected 2996350718U -160: file acs1996_3.svg gave hash 510450189U not the expected 879041204U -160: file acs1996_8.svg gave hash 3359655656U not the expected 4110469272U -160: file acs1996_10.svg gave hash 1008047306U not the expected 2229333301U -160: [03:09:56] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. -160: file bond_highlights_8.svg gave hash 197391689U not the expected 3119784980U 160: file test_github5947.svg gave hash 737562322U not the expected 3122633523U 160: file test_github6112.svg gave hash 3291975047U not the expected 3278777629U -51: Randomness seeded to: 2231542749 -51: =============================================================================== -51: All tests passed (14835 assertions in 14 test cases) -51: -158/236 Test #51: canonTestsCatch ........................ Passed 22.07 sec -test 170 - Start 170: testRascalMCES - -170: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES -170: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES -170: Test timeout computed to be: 1500 160: file github6336_1.png gave hash 1930712448U not the expected 2958833204U 160: file AtropManyChiralsEnhanced.svg gave hash 643650995U not the expected 2256768013U 160: file testWedgingShouldBeOnSingleBond.svg gave hash 2637422009U not the expected 1002741488U @@ -30329,7 +30348,18 @@ 160: =============================================================================== 160: All tests passed (6857 assertions in 116 test cases) 160: -159/236 Test #160: moldraw2DTestCatch ..................... Passed 5.45 sec +158/236 Test #160: moldraw2DTestCatch ..................... Passed 4.79 sec +test 170 + Start 170: testRascalMCES + +170: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES +170: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES +170: Test timeout computed to be: 1500 +51: Randomness seeded to: 4098991550 +51: =============================================================================== +51: All tests passed (14835 assertions in 14 test cases) +51: +159/236 Test #51: canonTestsCatch ........................ Passed 23.49 sec test 171 Start 171: testRascalCluster @@ -30338,42 +30368,64 @@ 171: Test timeout computed to be: 1500 169: ......... 169: ---------------------------------------------------------------------- -169: Ran 9 tests in 2.397s +169: Ran 9 tests in 2.815s 169: 169: OK -160/236 Test #169: pyMMPA ................................. Passed 3.09 sec +160/236 Test #169: pyMMPA ................................. Passed 3.36 sec test 172 Start 172: pyRascalMCES 172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" 172: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap 172: Test timeout computed to be: 1500 -172: ..........[03:09:59] Too many matching bond pairs (1032) so can't continue. -164: ........................................[03:10:01] The provided InitialSeed is not an MCS and will be ignored -164: [03:10:01] The provided InitialSeed is not an MCS and will be ignored -164: [03:10:01] The provided InitialSeed is not an MCS and will be ignored -164: .[03:10:01] The provided InitialSeed is not an MCS and will be ignored -164: [03:10:01] The provided InitialSeed is not an MCS and will be ignored -164: [03:10:01] The provided InitialSeed is not an MCS and will be ignored -164: .[03:10:01] The provided InitialSeed is not an MCS and will be ignored -164: [03:10:01] The provided InitialSeed is not an MCS and will be ignored -164: [03:10:01] The provided InitialSeed is not an MCS and will be ignored +164: ........................................[23:38:27] The provided InitialSeed is not an MCS and will be ignored +164: [23:38:27] The provided InitialSeed is not an MCS and will be ignored +164: [23:38:27] The provided InitialSeed is not an MCS and will be ignored +164: .[23:38:27] The provided InitialSeed is not an MCS and will be ignored +164: [23:38:27] The provided InitialSeed is not an MCS and will be ignored +164: [23:38:27] The provided InitialSeed is not an MCS and will be ignored +164: .[23:38:27] The provided InitialSeed is not an MCS and will be ignored +164: [23:38:27] The provided InitialSeed is not an MCS and will be ignored +164: [23:38:27] The provided InitialSeed is not an MCS and will be ignored +164: .[23:38:27] The provided InitialSeed is not an MCS and will be ignored +164: [23:38:27] The provided InitialSeed is not an MCS and will be ignored +164: [23:38:27] The provided InitialSeed is not an MCS and will be ignored +164: ................. +164: ---------------------------------------------------------------------- +164: Ran 60 tests in 5.134s +164: +164: OK +163: [23:38:27] The provided InitialSeed is not an MCS and will be ignored +161/236 Test #164: pyFMCS ................................. Passed 5.70 sec +test 173 + Start 173: testSynthonSpaceSubstructureSearch + +173: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch +173: Test timeout computed to be: 1500 +172: ..........[23:38:28] Too many matching bond pairs (1032) so can't continue. +173: Randomness seeded to: 3162848827 +173: [23:38:29] Writing the enumerated file may take quite some time and result in a large file. +172: .... +172: ---------------------------------------------------------------------- +172: Ran 14 tests in 2.002s +172: +172: OK +162/236 Test #172: pyRascalMCES ........................... Passed 2.85 sec +test 174 + Start 174: testSynthonSpaceRascalSearch + +174: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceRascalSearch +174: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch +174: Test timeout computed to be: 1500 159: Done 159: ----------------- Test Github #781: Rendering single-atom molecules 159: Done 159: ----------------- Test 3 159: file test3_1.png gave hash 3115155176U not the expected 675908852U -164: .[03:10:01] The provided InitialSeed is not an MCS and will be ignored -164: [03:10:01] The provided InitialSeed is not an MCS and will be ignored -164: [03:10:01] The provided InitialSeed is not an MCS and will be ignored 159: file test3_2.png gave hash 907411238U not the expected 2452584093U 159: file test3_3.png gave hash 2790716736U not the expected 1907006999U 159: file test3_3.svg gave hash 1119144208U not the expected 1375178959U -164: ................. -164: ---------------------------------------------------------------------- -164: Ran 60 tests in 7.131s -164: -164: OK 159: file test3_4.png gave hash 2163198482U not the expected 2305641511U 159: file test3_4.svg gave hash 2680534430U not the expected 187720898U 159: file test3_5.png gave hash 268184992U not the expected 3842605920U @@ -30390,13 +30442,6 @@ 159: Done 159: ----------------- Test Github852: Lines used to wedge bonds are too thick 159: file test852_1.png gave hash 172981142U not the expected 271517011U -161/236 Test #164: pyFMCS ................................. Passed 7.90 sec -test 173 - Start 173: testSynthonSpaceSubstructureSearch - -173: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch -173: Test timeout computed to be: 1500 159: file test852_2.png gave hash 330355316U not the expected 967452082U 159: ---------------- 159: ---------------- @@ -30442,6 +30487,7 @@ 159: ----------------- Testing use of continuous highlighting with drawMolecules 159: Done 159: ----------------- Test 17 - Testing maximum font size +173: [23:38:32] Building the fingerprints may take some time. 159: Done 159: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list 159: Done @@ -30460,24 +30506,12 @@ 159: ----------------- Testing testGithub2762: MolDraw2D: HCl and ethane should be drawn 159: Done 159: ----------------- Testing testGithub2931: multi-coloured molecule highlights. -172: .... -172: ---------------------------------------------------------------------- -172: Ran 14 tests in 2.458s -172: -172: OK 159: file testGithub2931_1.svg gave hash 608211058U not the expected 3635831631U 159: file testGithub2931_3.svg gave hash 1702246706U not the expected 2885834646U 159: Done 159: ----------------- Testing annotation of 2D Drawing. 159: file test20_1.png gave hash 2819944294U not the expected 200877868U 159: file test20_2.png gave hash 3331636090U not the expected 1651164846U -162/236 Test #172: pyRascalMCES ........................... Passed 3.41 sec -test 174 - Start 174: testSynthonSpaceRascalSearch - -174: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceRascalSearch -174: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch -174: Test timeout computed to be: 1500 159: file test20_3.png gave hash 4024902774U not the expected 1463603076U 159: file test20_4.png gave hash 2389521325U not the expected 1714613205U 159: Done @@ -30508,61 +30542,21 @@ 159: Done 159: ----------------- Test AND queries 159: Done -163/236 Test #159: moldraw2DTest1 ......................... Passed 10.30 sec +163/236 Test #159: moldraw2DTest1 ......................... Passed 11.31 sec test 175 Start 175: testCIPLabeler 175: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 175: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler 175: Test timeout computed to be: 1500 -175: Randomness seeded to: 1096017486 -175: [03:10:02] non kekulizable aromatic bond being treated as bond order 1 -175: [03:10:02] non kekulizable aromatic bond being treated as bond order 1 -175: [03:10:02] non kekulizable aromatic bond being treated as bond order 1 -175: [03:10:02] non kekulizable aromatic bond being treated as bond order 1 -175: [03:10:02] non kekulizable aromatic bond being treated as bond order 1 -175: [03:10:02] non kekulizable aromatic bond being treated as bond order 1 -175: [03:10:02] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -175: [03:10:02] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -175: =============================================================================== -175: All tests passed (6577 assertions in 19 test cases) -175: -164/236 Test #175: testCIPLabeler ......................... Passed 0.24 sec -test 176 - Start 176: pyCIPLabelsWrapTest - -176: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" -176: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap -176: Test timeout computed to be: 1500 -176: .... -176: ---------------------------------------------------------------------- -176: Ran 4 tests in 0.010s -176: -176: OK -165/236 Test #176: pyCIPLabelsWrapTest .................... Passed 0.26 sec -test 177 - Start 177: pyCIPLabelsValidation - -177: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" -177: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap -177: Test timeout computed to be: 1500 -173: Randomness seeded to: 2491108246 -173: [03:10:03] Writing the enumerated file may take quite some time and result in a large file. -173: [03:10:06] Building the fingerprints may take some time. -152: .............[03:10:06] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:10:06] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:10:06] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:10:06] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:10:06] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:10:06] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:10:06] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:10:06] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:10:06] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:10:06] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:10:06] Molecule does not have explicit Hs. Consider calling AddHs() -171: Randomness seeded to: 1487407390 -171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -173: [03:10:06] +175: Randomness seeded to: 745617382 +175: [23:38:32] non kekulizable aromatic bond being treated as bond order 1 +175: [23:38:32] non kekulizable aromatic bond being treated as bond order 1 +175: [23:38:32] non kekulizable aromatic bond being treated as bond order 1 +175: [23:38:32] non kekulizable aromatic bond being treated as bond order 1 +175: [23:38:32] non kekulizable aromatic bond being treated as bond order 1 +175: [23:38:32] non kekulizable aromatic bond being treated as bond order 1 +173: [23:38:32] 173: 173: **** 173: Invariant Violation @@ -30578,60 +30572,97 @@ 173: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 173: 5# RDKit::SynthonSpaceSearch::SynthonSet::makeSynthonSearchMols() in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 173: 6# RDKit::SynthonSpaceSearch::SynthonSpace::readTextFile(std::__cxx11::basic_string, std::allocator > const&, bool&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 -173: 7# 0x0000AAAAB6F7DB50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 8# 0x0000AAAAB6FC66EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 9# 0x0000AAAAB6FC70A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 10# 0x0000AAAAB6FC74D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 11# 0x0000AAAAB6F9A958 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 12# 0x0000AAAAB6F9AEA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 13# 0x0000AAAAB6F7CC10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 14# 0x0000FFFFB89F229C in /lib/aarch64-linux-gnu/libc.so.6 +173: 7# 0x0000AAAAD2BCDB50 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 8# 0x0000AAAAD2C166EC in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 9# 0x0000AAAAD2C170A0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 10# 0x0000AAAAD2C174D4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 11# 0x0000AAAAD2BEA958 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 12# 0x0000AAAAD2BEAEA4 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 13# 0x0000AAAAD2BCCC10 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 14# 0x0000FFFFB020229C in /lib/aarch64-linux-gnu/libc.so.6 173: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -173: 16# 0x0000AAAAB6F7CCF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 16# 0x0000AAAAD2BCCCF0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: ---------- 173: **** 173: -173: [03:10:06] Error:: in reaction amide-1 :: building molecule from synthons : 1-1 (c1cc[1*]ccc1C(=O)[1*]) and 2-1 ([1*]N1CCCC1) +173: [23:38:32] Error:: in reaction amide-1 :: building molecule from synthons : 1-1 (c1cc[1*]ccc1C(=O)[1*]) and 2-1 ([1*]N1CCCC1) 173: molzip: bond info not properly setup for bgn atom with label:1 -173: [03:10:06] Explicit valence for atom # 4 C, 5, is greater than permitted -173: [03:10:06] Error:: in reaction error-1 :: building molecule from synthons : 1-1 (C(=[2*])=CC=[1*]) and 2-1 (ClC([2*])=CN=[1*]) +173: [23:38:32] Explicit valence for atom # 4 C, 5, is greater than permitted +173: [23:38:32] Error:: in reaction error-1 :: building molecule from synthons : 1-1 (C(=[2*])=CC=[1*]) and 2-1 (ClC([2*])=CN=[1*]) 173: Explicit valence for atom # 4 C, 5, is greater than permitted -173: [03:10:06] Complex queries can be slow. -173: [03:10:06] Complex queries can be slow. -173: [03:10:07] Complex queries can be slow. -173: [03:10:07] Complex queries can be slow. -173: [03:10:07] Complex queries can be slow. -173: [03:10:07] Complex queries can be slow. -173: [03:10:08] Complex queries can be slow. -170: Randomness seeded to: 4022579884 -170: [03:10:08] Timed out after 11 seconds. -173: [03:10:08] Complex queries can be slow. -173: [03:10:08] Complex queries can be slow. -173: [03:10:09] Complex queries can be slow. -173: [03:10:09] Complex queries can be slow. -152: ...[03:10:10] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:10:10] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:10:10] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:10:10] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:10:10] Molecule does not have explicit Hs. Consider calling AddHs() +173: [23:38:32] Complex queries can be slow. +175: [23:38:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +175: [23:38:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +175: =============================================================================== +175: All tests passed (6577 assertions in 19 test cases) +175: +164/236 Test #175: testCIPLabeler ......................... Passed 0.28 sec +test 176 + Start 176: pyCIPLabelsWrapTest + +176: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" +176: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap +176: Test timeout computed to be: 1500 +173: [23:38:33] Complex queries can be slow. +173: [23:38:33] Complex queries can be slow. +176: .... +176: ---------------------------------------------------------------------- +176: Ran 4 tests in 0.022s +176: +176: OK +173: [23:38:33] Complex queries can be slow. +165/236 Test #176: pyCIPLabelsWrapTest .................... Passed 0.55 sec +test 177 + Start 177: pyCIPLabelsValidation + +177: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" +177: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap +177: Test timeout computed to be: 1500 +173: [23:38:33] Complex queries can be slow. +173: [23:38:33] Complex queries can be slow. +173: [23:38:34] Complex queries can be slow. +173: [23:38:34] Complex queries can be slow. +173: [23:38:34] Complex queries can be slow. +171: Randomness seeded to: 4169270657 +171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi +173: [23:38:34] Complex queries can be slow. +173: [23:38:35] Complex queries can be slow. +152: .............[23:38:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [23:38:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [23:38:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [23:38:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [23:38:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [23:38:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [23:38:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [23:38:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [23:38:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [23:38:36] Molecule does not have explicit Hs. Consider calling AddHs() +152: [23:38:36] Molecule does not have explicit Hs. Consider calling AddHs() +170: Randomness seeded to: 3392393786 +170: [23:38:37] Timed out after 11 seconds. +152: ...[23:38:39] Molecule does not have explicit Hs. Consider calling AddHs() +152: [23:38:39] Molecule does not have explicit Hs. Consider calling AddHs() +152: [23:38:39] Molecule does not have explicit Hs. Consider calling AddHs() +152: [23:38:39] Molecule does not have explicit Hs. Consider calling AddHs() +152: [23:38:39] Molecule does not have explicit Hs. Consider calling AddHs() 152: ... 152: ---------------------------------------------------------------------- -152: Ran 19 tests in 20.076s +152: Ran 19 tests in 20.270s 152: 152: OK 152: Testing MolAlign Wrappers -166/236 Test #152: pyMolAlign ............................. Passed 20.71 sec +166/236 Test #152: pyMolAlign ............................. Passed 20.90 sec test 178 Start 178: deprotectTest 178: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 178: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect 178: Test timeout computed to be: 1500 -178: Randomness seeded to: 2072741918 +178: Randomness seeded to: 1350630878 178: =============================================================================== 178: All tests passed (111 assertions in 3 test cases) 178: -167/236 Test #178: deprotectTest .......................... Passed 0.14 sec +167/236 Test #178: deprotectTest .......................... Passed 0.10 sec test 179 Start 179: pyDeprotect @@ -30640,7 +30671,7 @@ 179: Test timeout computed to be: 1500 179: ..... 179: ---------------------------------------------------------------------- -179: Ran 5 tests in 0.088s +179: Ran 5 tests in 0.071s 179: 179: OK 179: Testing tert-butyldimethylsilyl @@ -30693,7 +30724,7 @@ 179: Testing acetamide 179: Testing carbobenzyloxy 179: Testing Acetal/Ketal -168/236 Test #179: pyDeprotect ............................ Passed 0.82 sec +168/236 Test #179: pyDeprotect ............................ Passed 0.69 sec test 180 Start 180: testReducedGraphs @@ -30718,13 +30749,76 @@ 180: 180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 180: -169/236 Test #180: testReducedGraphs ...................... Passed 0.05 sec +169/236 Test #180: testReducedGraphs ...................... Passed 0.07 sec test 181 Start 181: pyReducedGraphs 181: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" 181: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap 181: Test timeout computed to be: 1500 +181: ..... +181: ---------------------------------------------------------------------- +181: Ran 5 tests in 0.029s +181: +181: OK +170/236 Test #181: pyReducedGraphs ........................ Passed 0.57 sec +test 182 + Start 182: trajectoryTest + +182: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest +182: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory +182: Test timeout computed to be: 1500 +171/236 Test #182: trajectoryTest ......................... Passed 0.46 sec +test 183 + Start 183: substructLibraryTest + +183: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest +183: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary +183: Test timeout computed to be: 1500 +183: [23:38:42] ------------------------------------- +183: [23:38:42] Test1 +183: [23:38:42] done +183: [23:38:42] ------------------------------------- +183: [23:38:42] Test2 +183: [23:38:42] done +183: [23:38:42] ------------------------------------- +183: [23:38:42] Test3 (stereo options) +183: [23:38:43] Done (stereo options) +183: [23:38:43] ------------------------------------- +183: [23:38:43] Test4 (trusted smiles) +183: [23:38:43] Done (trusted smiles) +183: [23:38:43] ------------------------------------- +183: [23:38:43] Testing C++ docs +183: [23:38:43] Done (C++ doc tests) +183: [23:38:43] ------------------------------------- +183: [23:38:43] Testing C++ ring query: PatternHolder +183: [23:38:43] Done (C++ ring query tests) +183: [23:38:43] ------------------------------------- +183: [23:38:43] Testing C++ ring query: TautomerPatternHolder +183: [23:38:43] Done (C++ ring query tests) +183: [23:38:43] ------------------------------------- +183: [23:38:43] Add Patterns +148: .........[23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() +148: [23:38:43] Molecule does not have explicit Hs. Consider calling AddHs() 177: VS001: PASSED 177: VS002: PASSED 177: VS003: PASSED @@ -31027,109 +31121,27 @@ 177: VS300: PASSED 177: Check finished: 0 molecules failed. 177: Failed: -170/236 Test #177: pyCIPLabelsValidation .................. Passed 9.39 sec -test 182 - Start 182: trajectoryTest - -182: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest -182: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory -182: Test timeout computed to be: 1500 -181: ..... -181: ---------------------------------------------------------------------- -181: Ran 5 tests in 0.020s -181: -181: OK -171/236 Test #181: pyReducedGraphs ........................ Passed 0.47 sec -test 183 - Start 183: substructLibraryTest - -183: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest -183: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary -183: Test timeout computed to be: 1500 -183: [03:10:12] ------------------------------------- -183: [03:10:12] Test1 -172/236 Test #182: trajectoryTest ......................... Passed 0.60 sec +172/236 Test #177: pyCIPLabelsValidation .................. Passed 9.77 sec test 184 Start 184: substructLibraryCatchTest 184: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 184: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 184: Test timeout computed to be: 1500 -183: [03:10:13] done -183: [03:10:13] ------------------------------------- -183: [03:10:13] Test2 -183: [03:10:13] done -183: [03:10:13] ------------------------------------- -183: [03:10:13] Test3 (stereo options) -183: [03:10:13] Done (stereo options) -183: [03:10:13] ------------------------------------- -183: [03:10:13] Test4 (trusted smiles) -183: [03:10:13] Done (trusted smiles) -183: [03:10:13] ------------------------------------- -183: [03:10:13] Testing C++ docs -183: [03:10:13] Done (C++ doc tests) -183: [03:10:13] ------------------------------------- -183: [03:10:13] Testing C++ ring query: PatternHolder -183: [03:10:13] Done (C++ ring query tests) -183: [03:10:13] ------------------------------------- -183: [03:10:13] Testing C++ ring query: TautomerPatternHolder -183: [03:10:13] Done (C++ ring query tests) -183: [03:10:13] ------------------------------------- -183: [03:10:13] Add Patterns 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 20.47 seconds -173/236 Test #163: testFMCS ............................... Passed 20.58 sec +163: TOTAL Time elapsed 21.17 seconds +173/236 Test #163: testFMCS ............................... Passed 21.23 sec test 185 Start 185: pySubstructLibrary 185: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" 185: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 185: Test timeout computed to be: 1500 -184: Randomness seeded to: 346466502 -184: =============================================================================== -184: All tests passed (171 assertions in 5 test cases) -184: -174/236 Test #184: substructLibraryCatchTest .............. Passed 1.86 sec -test 186 - Start 186: testRGroupDecomp - -186: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp -186: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition -186: Test timeout computed to be: 1500 -186: [03:10:15] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -186: [03:10:15] WARNING: not removing hydrogen atom with dummy atom neighbors -148: .........[03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:10:17] Molecule does not have explicit Hs. Consider calling AddHs() -173: [03:10:18] Complex queries can be slow. -173: [03:10:18] Complex queries can be slow. -173: [03:10:18] Complex queries can be slow. -173: [03:10:18] Complex queries can be slow. -173: [03:10:18] Complex queries can be slow. -173: [03:10:19] Complex queries can be slow. 150: --------------------------------- 150: test O3A multithreading bug 150: @@ -31137,1116 +31149,634 @@ 150: testCrippenO3A multithreading 150: 150: generating reference data -173: [03:10:19] Complex queries can be slow. -186: iterative -173: [03:10:19] Complex queries can be slow. -183: [03:10:19] ------------------------------------- -183: [03:10:19] testing PatternHolder -173: [03:10:19] Complex queries can be slow. -183: [03:10:19] ------------------------------------- -183: [03:10:19] testing TautomerPatternHolder -183: [03:10:20] ------------------------------------- -183: [03:10:20] testSegFaultInHolder -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] 1SMILES Parse Error: syntax error while parsing: dsafsdf: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] [03:10:20] dsafsdf -183: SMILES[03:10:20] SMILES Parse Error: -183: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: syntax error Parse Error: Failed parsing SMILES 'dsafsdf' while parsing: [03:10:20] dsafsdf for input: 'dsafsdf' -183: -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -186: bulk -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILESSMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdfFailed parsing SMILES 'dsafsdf'[03:10:20] SMILES Parse Error: syntax error[03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: while parsing: [03:10:20] -183: [03:10:20] ^dsafsdfdsafsdf -183: -183: -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[03:10:20] for input: '[03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:10:20] SMILES Parse Error: check for mistakes around position 1: -183: [03:10:20] dsafsdf -183: [03:10:20] ^ -183: [03:10:20] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:10:20] ------------------------------------- -183: [03:10:20] Results do not depend on numThreads 150: processing 150: launch :0 150: launch :1 150: launch :2 150: launch :3 -173: [03:10:20] Complex queries can be slow. -173: [03:10:20] Complex queries can be slow. -173: [03:10:21] Complex queries can be slow. -173: [03:10:21] Complex queries can be slow. -173: [03:10:22] Complex queries can be slow. -186: bulk, no symmetry -173: [03:10:23] Complex queries can be slow. +184: Randomness seeded to: 4125955667 +184: =============================================================================== +184: All tests passed (171 assertions in 5 test cases) +184: +174/236 Test #184: substructLibraryCatchTest .............. Passed 1.51 sec +test 186 + Start 186: testRGroupDecomp + +186: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp +186: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition +186: Test timeout computed to be: 1500 +186: [23:38:45] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +186: [23:38:45] WARNING: not removing hydrogen atom with dummy atom neighbors +173: [23:38:45] Complex queries can be slow. +173: [23:38:46] Complex queries can be slow. +173: [23:38:46] Complex queries can be slow. +173: [23:38:46] Complex queries can be slow. 148: ... 148: ---------------------------------------------------------------------- -148: Ran 22 tests in 34.137s +148: Ran 22 tests in 28.146s 148: 148: OK -175/236 Test #148: pyDistGeomHelpers ...................... Passed 34.89 sec +175/236 Test #148: pyDistGeomHelpers ...................... Passed 28.93 sec test 187 Start 187: testRGroupDecompInternals 187: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 187: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 187: Test timeout computed to be: 1500 -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:10:23] WARNING: not removing hydrogen atom with dummy atom neighbors -176/236 Test #187: testRGroupDecompInternals .............. Passed 0.06 sec +173: [23:38:46] Complex queries can be slow. +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [23:38:46] WARNING: not removing hydrogen atom with dummy atom neighbors +176/236 Test #187: testRGroupDecompInternals .............. Passed 0.05 sec test 188 Start 188: rgroupCatchTests 188: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 188: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 188: Test timeout computed to be: 1500 -186: [03:10:23] Relabelling existing label -173: [03:10:23] Complex queries can be slow. -186: Best mapping -177/236 Test #186: testRGroupDecomp ....................... Passed 8.99 sec +173: [23:38:46] Complex queries can be slow. +173: [23:38:46] Complex queries can be slow. +188: Randomness seeded to: 1366155561 +188: =============================================================================== +188: All tests passed (1475 assertions in 14 test cases) +188: +177/236 Test #188: rgroupCatchTests ....................... Passed 0.36 sec test 189 Start 189: pyRGroupDecomposition 189: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 189: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 189: Test timeout computed to be: 1500 -173: [03:10:23] Complex queries can be slow. -188: Randomness seeded to: 3110638791 -188: =============================================================================== -188: All tests passed (1475 assertions in 14 test cases) -188: -178/236 Test #188: rgroupCatchTests ....................... Passed 0.87 sec +173: [23:38:47] Complex queries can be slow. +173: [23:38:47] Complex queries can be slow. +173: [23:38:47] Complex queries can be slow. +173: [23:38:47] Complex queries can be slow. +186: iterative +173: [23:38:47] Complex queries can be slow. +173: [23:38:47] Complex queries can be slow. +173: [23:38:48] Complex queries can be slow. +183: [23:38:48] ------------------------------------- +183: [23:38:48] testing PatternHolder +173: [23:38:48] Complex queries can be slow. +186: bulk +183: [23:38:48] ------------------------------------- +183: [23:38:48] testing TautomerPatternHolder +173: [23:38:48] Complex queries can be slow. +189: .................... +189: ---------------------------------------------------------------------- +189: Ran 20 tests in 1.114s +189: +189: OK +178/236 Test #189: pyRGroupDecomposition .................. Passed 1.72 sec +183: [23:38:48] ------------------------------------- +183: [23:38:48] testSegFaultInHolder test 190 Start 190: molInterchangeTest1 190: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 190: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 190: Test timeout computed to be: 1500 -190: [03:10:24] test1: basics -190: [03:10:24] done -190: [03:10:24] test2: basic writing +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] dsafsdf +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] [23:38:48] [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1:SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'syntax error while parsing: dsafsdf[23:38:48] +183: dsafsdf' +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: dsafsdf[23:38:48] [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: SMILES Parse Error: SMILES Parse Error: check for mistakes around position syntax error[23:38:48] while parsing: dsafsdf +183: 1[23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: check for mistakes around position 1 +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] :[23:38:48] SMILES Parse Error: syntax errorsyntax errordsafsdf while parsing: dsafsdf +183: [23:38:48] +183: +183: :[23:38:48] +183: [23:38:48] dsafsdf +183: dsafsdf +183: while parsing: dsafsdf +183: [23:38:48] [23:38:48] ^^[23:38:48] SMILES Parse Error: check for mistakes around position +183: +183: [23:38:48] SMILES[23:38:48] 1: +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '^ +183: [23:38:48] dsafsdf Parse Error: Failed parsing SMILES 'dsafsdf' for input: ' +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[23:38:48] dsafsdf' +183: dsafsdf' +183: ' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position [23:38:48] dsafsdf +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'1: +183: for input: '[23:38:48] SMILES Parse Error: check for mistakes around position SMILES Parse Error: syntax error while parsing: [23:38:48] dsafsdfdsafsdf1: +183: +183: [23:38:48] ^ +183: dsafsdf' +183: +183: [23:38:48] [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: : +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf[23:38:48] [23:38:48] SMILES Parse Error: check for mistakes around position 1:[23:38:48] SMILES Parse Error: check for mistakes around position 1 +183: SMILES Parse Error: syntax error while parsing: [23:38:48] : +183: dsafsdfdsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position +183: [23:38:48] ^[23:38:48] dsafsdf +183: +183: [23:38:48] ^1: +183: [23:38:48] ^ +183: [23:38:48] SMILES[23:38:48] +183: [23:38:48] +183: dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'SMILES Parse Error: dsafsdf'Failed parsing SMILES 'dsafsdf'dsafsdf' for input: ' +183: dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +190: [23:38:48] test1: basics +190: [23:38:48] done +190: [23:38:48] test2: basic writing 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,0]}]}]} 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","aromaticAtoms":[0,1,2,3,4,5],"aromaticBonds":[0,1,2,3,4,5],"cipRanks":[0,0,0,0,0,0],"atomRings":[[0,5,4,3,2,1]]}]}]} 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","aromaticAtoms":[2,3,5,6,8,9],"aromaticBonds":[2,4,5,7,8,9],"cipRanks":[0,2,4,5,8,3,7,1,9,6],"atomRings":[[2,9,8,6,5,3]]}]}]} -190: [03:10:24] done -190: [03:10:24] test3: writing conformers +190: [23:38:48] done +190: [23:38:48] test3: writing conformers 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1988,-0.0452],[-0.3332,0.4556],[0.166,1.322],[0.5332,-0.0438],[-2.0652,0.4542],[-0.834,1.3212]]},{"dim":3,"coords":[[0.9554,-0.3743,-0.4679],[-0.3616,-0.1311,-0.0795],[-0.5097,1.6256,0.1706],[-0.5779,-0.792,1.1042],[1.5277,0.1064,0.1628],[-1.0339,-0.4346,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2025.03.1","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} -190: [03:10:24] done -190: [03:10:24] test4: writing properties +190: [23:38:48] done +190: [23:38:48] test4: writing properties 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"properties":{"foo_string":"bar","foo_int":1,"foo_double":1.2},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,0]}]}]} -190: [03:10:24] done -190: [03:10:24] test5: writing partial charges +190: [23:38:48] done +190: [23:38:48] test5: writing partial charges 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"z":8,"impHs":1}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2025.03.1","values":[0.5,-0.5]}]}]} -190: [03:10:24] testing parse options -190: [03:10:24] done -190: [03:10:24] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +190: [23:38:48] testing parse options +190: [23:38:48] done +190: [23:38:48] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 190: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":2},{"impHs":2},{"impHs":2},{"z":8},{"impHs":1,"stereo":"cw"},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -190: [03:10:24] done -190: [03:10:24] testing 'either' stereochemistry -190: [03:10:24] done +190: [23:38:48] done +190: [23:38:48] testing 'either' stereochemistry +190: [23:38:48] done 179/236 Test #190: molInterchangeTest1 .................... Passed 0.05 sec test 191 Start 191: molInterchangeCatchTest @@ -32254,9 +31784,512 @@ 191: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 191: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 191: Test timeout computed to be: 1500 -191: Randomness seeded to: 3981281404 -191: [03:10:24] unrecognized bond type 12 set to zero while writing -191: [03:10:24] unrecognized bond type 0 set to zero while writing +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [23:38:48] SMILES Parse Error: check for mistakes around position 1: +183: [23:38:48] dsafsdf +183: [23:38:48] ^ +183: [23:38:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [23:38:48] ------------------------------------- +183: [23:38:48] Results do not depend on numThreads +173: [23:38:48] Complex queries can be slow. +191: Randomness seeded to: 2483581874 +191: [23:38:48] unrecognized bond type 12 set to zero while writing +191: [23:38:48] unrecognized bond type 0 set to zero while writing 191: =============================================================================== 191: All tests passed (125 assertions in 7 test cases) 191: @@ -32267,23 +32300,19 @@ 192: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 192: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 192: Test timeout computed to be: 1500 -173: [03:10:24] Complex queries can be slow. -173: [03:10:24] Complex queries can be slow. -173: =============================================================================== -173: All tests passed (121 assertions in 17 test cases) -173: -181/236 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 22.94 sec +192: .. +192: ---------------------------------------------------------------------- +192: Ran 2 tests in 0.007s +192: +192: OK +173: [23:38:48] Complex queries can be slow. +181/236 Test #192: pyMolInterchange ....................... Passed 0.21 sec test 193 Start 193: testSLNParse 193: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 193: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse 193: Test timeout computed to be: 1500 -192: .. -192: ---------------------------------------------------------------------- -192: Ran 2 tests in 0.016s -192: -192: OK 193: Atoms: 193: 0 6 C chg: 1 deg: 5 exp: N/A imp: 0 hyb: 193: 1 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: @@ -32297,20 +32326,20 @@ 193: 2 0->3 order: 1 193: 3 0->4 order: 1 193: 4 0->5 order: 1 -193: [03:10:24] SLN Parse Error: syntax error while parsing: CH4[I=13] -193: [03:10:24] Failed parsing SLN 'CH4[I=13]' -193: [03:10:24] SLN Parser error: Atom ID 1 appears *after* its ring closure. -193: [03:10:24] SLN Parser error: Ring closure 1 does not have a corresponding opener. -193: [03:10:24] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -193: [03:10:24] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -193: [03:10:24] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -193: [03:10:24] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -193: [03:10:24] SLN Parse Error: syntax error while parsing: CH4 fff -193: [03:10:24] Failed parsing SLN 'CH4 fff' -193: [03:10:24] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -193: [03:10:24] Failed parsing SLN 'C[charge=+1] foo' -193: [03:10:24] Query property 'is' ignored on non-query atom -193: [03:10:24] Query property 'is' ignored on non-query atom +193: [23:38:48] SLN Parse Error: syntax error while parsing: CH4[I=13] +193: [23:38:48] Failed parsing SLN 'CH4[I=13]' +193: [23:38:48] SLN Parser error: Atom ID 1 appears *after* its ring closure. +193: [23:38:48] SLN Parser error: Ring closure 1 does not have a corresponding opener. +193: [23:38:48] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +193: [23:38:48] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +193: [23:38:48] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +193: [23:38:48] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +193: [23:38:48] SLN Parse Error: syntax error while parsing: CH4 fff +193: [23:38:48] Failed parsing SLN 'CH4 fff' +193: [23:38:48] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +193: [23:38:48] Failed parsing SLN 'C[charge=+1] foo' +193: [23:38:48] Query property 'is' ignored on non-query atom +193: [23:38:48] Query property 'is' ignored on non-query atom 182/236 Test #193: testSLNParse ........................... Passed 0.02 sec test 194 Start 194: pySLNParse @@ -32318,67 +32347,71 @@ 194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap/testSLN.py" 194: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap 194: Test timeout computed to be: 1500 -183/236 Test #192: pyMolInterchange ....................... Passed 0.48 sec +194: .. +194: ---------------------------------------------------------------------- +194: Ran 2 tests in 0.007s +194: +194: OK +173: [23:38:49] Complex queries can be slow. +183/236 Test #194: pySLNParse ............................. Passed 0.22 sec test 195 Start 195: pyGraphMolWrap 195: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rough_test.py" 195: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 195: Test timeout computed to be: 1500 -194: .. -194: ---------------------------------------------------------------------- -194: Ran 2 tests in 0.026s -194: -194: OK -184/236 Test #194: pySLNParse ............................. Passed 0.64 sec +173: =============================================================================== +173: All tests passed (121 assertions in 17 test cases) +173: +184/236 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 21.26 sec test 196 Start 196: pyTestConformerWrap 196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testConformer.py" 196: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 196: Test timeout computed to be: 1500 -195: ..............[03:10:25] SMARTS Parse Error: syntax error while parsing: fiib -195: [03:10:25] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -195: ....[03:10:25] ERROR: Problems encountered parsing data fields -195: [03:10:25] ERROR: moving to the beginning of the next molecule -195: [03:10:25] ERROR: Problems encountered parsing data fields -195: [03:10:25] ERROR: moving to the beginning of the next molecule -195: [03:10:25] Spurious data before the first property will be ignored -195: [03:10:25] Property will be truncated after the first blank line -195: [03:10:25] Property will be truncated after the first blank line -195: [03:10:25] Property will be truncated after the first blank line -195: [03:10:25] ERROR: Problems encountered parsing data fields -195: [03:10:25] ERROR: moving to the beginning of the next molecule -195: [03:10:25] ERROR: Problems encountered parsing data fields -195: [03:10:25] ERROR: moving to the beginning of the next molecule -195: [03:10:25] Spurious data before the first property will be ignored -195: [03:10:25] Property will be truncated after the first blank line -195: [03:10:25] Property will be truncated after the first blank line -195: [03:10:25] Property will be truncated after the first blank line -195: [03:10:25] ERROR: Problems encountered parsing data fields -195: [03:10:25] ERROR: moving to the beginning of the next molecule -195: [03:10:25] Property will be truncated after the first blank line -195: [03:10:25] ERROR: Problems encountered parsing data fields -195: [03:10:25] ERROR: moving to the beginning of the next molecule -195: [03:10:25] Property will be truncated after the first blank line -195: .[03:10:25] SMILES Parse Error: syntax error while parsing: fail -195: [03:10:25] SMILES Parse Error: check for mistakes around position 1: -195: [03:10:25] fail -195: [03:10:25] ^ -195: [03:10:25] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -195: [03:10:25] ERROR: Smiles parse error on line 2 -195: [03:10:25] ERROR: Cannot create molecule from : 'fail' +195: ..............[23:38:49] SMARTS Parse Error: syntax error while parsing: fiib +195: [23:38:49] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +195: ....[23:38:49] ERROR: Problems encountered parsing data fields +195: [23:38:49] ERROR: moving to the beginning of the next molecule +195: [23:38:49] ERROR: Problems encountered parsing data fields +195: [23:38:49] ERROR: moving to the beginning of the next molecule +195: [23:38:49] Spurious data before the first property will be ignored +195: [23:38:49] Property will be truncated after the first blank line +195: [23:38:49] Property will be truncated after the first blank line +195: [23:38:49] Property will be truncated after the first blank line +195: [23:38:49] ERROR: Problems encountered parsing data fields +195: [23:38:49] ERROR: moving to the beginning of the next molecule +195: [23:38:49] ERROR: Problems encountered parsing data fields +195: [23:38:49] ERROR: moving to the beginning of the next molecule +195: [23:38:49] Spurious data before the first property will be ignored +195: [23:38:49] Property will be truncated after the first blank line +195: [23:38:49] Property will be truncated after the first blank line +195: [23:38:49] Property will be truncated after the first blank line +195: [23:38:49] ERROR: Problems encountered parsing data fields +195: [23:38:49] ERROR: moving to the beginning of the next molecule +195: [23:38:49] Property will be truncated after the first blank line +195: [23:38:49] ERROR: Problems encountered parsing data fields +195: [23:38:49] ERROR: moving to the beginning of the next molecule +195: [23:38:49] Property will be truncated after the first blank line +195: .[23:38:49] SMILES Parse Error: syntax error while parsing: fail +195: [23:38:49] SMILES Parse Error: check for mistakes around position 1: +195: [23:38:49] fail +195: [23:38:49] ^ +195: [23:38:49] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +195: [23:38:49] ERROR: Smiles parse error on line 2 +195: [23:38:49] ERROR: Cannot create molecule from : 'fail' 195: >>> This may result in an infinite loop. It should finish almost instantly 195: <<< OK, it finished. -195: ............[03:10:25] Explicit valence for atom # 1 C, 5, is greater than permitted -195: ......[03:10:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: [03:10:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: [03:10:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -195: [03:10:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: ............[23:38:49] Explicit valence for atom # 1 C, 5, is greater than permitted +195: ......[23:38:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [23:38:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [23:38:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +195: [23:38:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 195: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| -195: ........[03:10:25] non-ring atom 0 marked aromatic -195: [03:10:25] non-ring atom 0 marked aromatic -195: [03:10:25] +195: ........[23:38:49] non-ring atom 0 marked aromatic +195: [23:38:49] non-ring atom 0 marked aromatic +195: [23:38:49] 195: 195: **** 195: Range Error @@ -32391,9 +32424,9 @@ 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 4# 0x0000FFFFAD6055F0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 4# 0x0000FFFF95BA55F0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 6# 0x0000FFFFAF002680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 6# 0x0000FFFF975A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -32404,17 +32437,17 @@ 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAD53C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAD53C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAD53C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAD53C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x0000FFFFAD53C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF95ADC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF95ADC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF95ADC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF95ADC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x0000FFFF95ADC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 27# 0x0000FFFFAEFFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 27# 0x0000FFFF9759F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 28# _PyObject_MakeTpCall in /usr/bin/python3 195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 30# 0x0000000000536550 in /usr/bin/python3 @@ -32446,15 +32479,15 @@ 195: 56# 0x0000000000628F70 in /usr/bin/python3 195: 57# Py_RunMain in /usr/bin/python3 195: 58# Py_BytesMain in /usr/bin/python3 -195: 59# 0x0000FFFFAFD4229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 59# 0x0000FFFF982E229C in /lib/aarch64-linux-gnu/libc.so.6 195: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 61# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [03:10:25] non-ring atom 0 marked aromatic -195: [03:10:25] non-ring atom 0 marked aromatic -195: [03:10:25] +195: [23:38:49] non-ring atom 0 marked aromatic +195: [23:38:49] non-ring atom 0 marked aromatic +195: [23:38:49] 195: 195: **** 195: Range Error @@ -32467,9 +32500,9 @@ 195: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -195: 4# 0x0000FFFFAD6055F0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 4# 0x0000FFFF95BA55F0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 6# 0x0000FFFFAF002680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 6# 0x0000FFFF975A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -32480,17 +32513,17 @@ 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAD53C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAD53C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAD53C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAD53C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x0000FFFFAD53C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF95ADC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF95ADC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF95ADC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF95ADC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x0000FFFF95ADC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 27# 0x0000FFFFAEFFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 27# 0x0000FFFF9759F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 28# _PyObject_MakeTpCall in /usr/bin/python3 195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 30# 0x0000000000536550 in /usr/bin/python3 @@ -32522,27 +32555,30 @@ 195: 56# 0x0000000000628F70 in /usr/bin/python3 195: 57# Py_RunMain in /usr/bin/python3 195: 58# Py_BytesMain in /usr/bin/python3 -195: 59# 0x0000FFFFAFD4229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 59# 0x0000FFFF982E229C in /lib/aarch64-linux-gnu/libc.so.6 195: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 61# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: ...............[03:10:25] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -195: [03:10:25] 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. -183: [03:10:25] ------------------------------------- -183: [03:10:25] Results do not depend on numThreads (all same) -195: ..............[03:10:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -195: [03:10:25] Explicit valence for atom # 1 C, 5, is greater than permitted +195: ...............[23:38:49] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +195: [23:38:49] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +195: ..............[23:38:49] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +195: [23:38:49] Explicit valence for atom # 1 C, 5, is greater than permitted 196: ...... 196: ---------------------------------------------------------------------- -196: Ran 6 tests in 0.029s +196: Ran 6 tests in 0.021s 196: 196: OK -195: ............................[03:10:25] unable to set wavy bonds for double bonds: 3 -183: [03:10:25] ------------------------------------- -183: [03:10:25] testTautomerQueries -195: .............[03:10:25] +185/236 Test #196: pyTestConformerWrap .................... Passed 0.49 sec +test 197 + Start 197: pyTestTrajectory + +197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testTrajectory.py" +197: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +197: Test timeout computed to be: 1500 +195: ............................[23:38:49] unable to set wavy bonds for double bonds: 3 +195: .............[23:38:49] 195: 195: **** 195: Range Error @@ -32557,7 +32593,7 @@ 195: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 6# 0x0000FFFFAF002680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 6# 0x0000FFFF975A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -32568,17 +32604,17 @@ 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAD53C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAD53C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAD53C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAD53C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 21# 0x0000FFFFAD53C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF95ADC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF95ADC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF95ADC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF95ADC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 21# 0x0000FFFF95ADC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 27# 0x0000FFFFAEFFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 27# 0x0000FFFF9759F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 28# _PyObject_MakeTpCall in /usr/bin/python3 195: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 30# 0x0000000000536550 in /usr/bin/python3 @@ -32610,43 +32646,13 @@ 195: 56# 0x0000000000628F70 in /usr/bin/python3 195: 57# Py_RunMain in /usr/bin/python3 195: 58# Py_BytesMain in /usr/bin/python3 -195: 59# 0x0000FFFFAFD4229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 59# 0x0000FFFF982E229C in /lib/aarch64-linux-gnu/libc.so.6 195: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 61# _start in /usr/bin/python3 195: ---------- 195: **** 195: -183: [03:10:25] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -183: [03:10:25] ------------------------------------- -183: [03:10:25] github3881 recursive smarts with rings -185/236 Test #183: substructLibraryTest ................... Passed 13.15 sec -test 197 - Start 197: pyTestTrajectory - -197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testTrajectory.py" -197: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -197: Test timeout computed to be: 1500 -186/236 Test #196: pyTestConformerWrap .................... Passed 0.73 sec -test 198 - Start 198: pyTestSGroups - -198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testSGroups.py" -198: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -198: Test timeout computed to be: 1500 -198: ............. -198: ---------------------------------------------------------------------- -198: Ran 13 tests in 0.014s -198: -198: OK -198: Testing SubstanceGroups wrapper -187/236 Test #198: pyTestSGroups .......................... Passed 0.28 sec -test 199 - Start 199: pyTestThreads - -199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testThreads.py" -199: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -199: Test timeout computed to be: 1500 -197: [03:10:26] +197: [23:38:50] 197: 197: **** 197: Pre-condition Violation @@ -32660,23 +32666,23 @@ 197: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF88162680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB8962680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFF8673C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFF8673C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFF8673C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFF8673C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFF8673C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFFB6F3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFFB6F3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFFB6F3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFFB6F3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFFB6F3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFF8815F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFFB895F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x0000000000536550 in /usr/bin/python3 @@ -32708,13 +32714,13 @@ 197: 50# 0x0000000000628F70 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFF8894229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFFB914229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[03:10:26] +197: .[23:38:50] 197: 197: **** 197: Pre-condition Violation @@ -32728,23 +32734,23 @@ 197: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF88162680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB8962680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFF8673C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFF8673C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFF8673C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFF8673C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFF8673C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFFB6F3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFFB6F3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFFB6F3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFFB6F3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFFB6F3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFF8815F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFFB895F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x0000000000536550 in /usr/bin/python3 @@ -32776,25 +32782,13 @@ 197: 50# 0x0000000000628F70 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFF8894229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFFB914229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -189: .................... -189: ---------------------------------------------------------------------- -189: Ran 20 tests in 2.391s -189: -189: OK -188/236 Test #189: pyRGroupDecomposition .................. Passed 2.93 sec -test 200 - Start 200: pyTestMultithreadedMolSupplier - -200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" -200: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -200: Test timeout computed to be: 1500 -197: .[03:10:27] +197: .[23:38:50] 197: 197: **** 197: Range Error @@ -32809,23 +32803,23 @@ 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x0000FFFF88162680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x0000FFFFB8962680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFF8673C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFF8673C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFF8673C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFF8673C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF8673C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFFB6F3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFFB6F3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFFB6F3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFFB6F3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFB6F3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# 0x0000FFFF8815F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x0000FFFFB895F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x0000000000536550 in /usr/bin/python3 @@ -32857,13 +32851,13 @@ 197: 51# 0x0000000000628F70 in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 -197: 54# 0x0000FFFF8894229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 54# 0x0000FFFFB914229C in /lib/aarch64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[03:10:27] +197: .[23:38:50] 197: 197: **** 197: Pre-condition Violation @@ -32877,23 +32871,23 @@ 197: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF88162680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB8962680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFF8673C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFF8673C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFF8673C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFF8673C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFF8673C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFFB6F3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFFB6F3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFFB6F3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFFB6F3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFFB6F3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFF8815F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFFB895F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x0000000000536550 in /usr/bin/python3 @@ -32925,13 +32919,13 @@ 197: 50# 0x0000000000628F70 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFF8894229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFFB914229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: ..[03:10:27] +197: ..[23:38:50] 197: 197: **** 197: Pre-condition Violation @@ -32945,23 +32939,23 @@ 197: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF88162680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB8962680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFF8673C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFF8673C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFF8673C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFF8673C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFF8673C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFFB6F3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFFB6F3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFFB6F3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFFB6F3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFFB6F3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFF8815F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFFB895F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x0000000000536550 in /usr/bin/python3 @@ -32993,13 +32987,13 @@ 197: 50# 0x0000000000628F70 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFF8894229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFFB914229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[03:10:27] +197: .[23:38:50] 197: 197: **** 197: Pre-condition Violation @@ -33013,23 +33007,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF88162680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB8962680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFF8673C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFF8673C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFF8673C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFF8673C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFF8673C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFFB6F3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFFB6F3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFFB6F3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFFB6F3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFFB6F3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFF8815F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFFB895F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x0000000000536550 in /usr/bin/python3 @@ -33061,13 +33055,13 @@ 197: 50# 0x0000000000628F70 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFF8894229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFFB914229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [03:10:27] +197: [23:38:50] 197: 197: **** 197: Pre-condition Violation @@ -33081,23 +33075,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF88162680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB8962680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFF8673C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFF8673C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFF8673C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFF8673C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFF8673C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFFB6F3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFFB6F3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFFB6F3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFFB6F3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFFB6F3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFF8815F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFFB895F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x0000000000536550 in /usr/bin/python3 @@ -33129,13 +33123,13 @@ 197: 50# 0x0000000000628F70 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFF8894229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFFB914229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[03:10:27] +197: .[23:38:50] 197: 197: **** 197: Range Error @@ -33150,23 +33144,23 @@ 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x0000FFFF88162680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x0000FFFFB8962680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFF8673C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFF8673C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFF8673C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFF8673C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF8673C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFFB6F3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFFB6F3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFFB6F3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFFB6F3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFB6F3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# 0x0000FFFF8815F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x0000FFFFB895F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x0000000000536550 in /usr/bin/python3 @@ -33198,13 +33192,13 @@ 197: 51# 0x0000000000628F70 in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 -197: 54# 0x0000FFFF8894229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 54# 0x0000FFFFB914229C in /lib/aarch64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [03:10:27] +197: [23:38:50] 197: 197: **** 197: Range Error @@ -33218,23 +33212,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF88162680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB8962680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFF8673C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFF8673C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFF8673C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFF8673C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFF8673C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFFB6F3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFFB6F3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFFB6F3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFFB6F3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFFB6F3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFF8815F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFFB895F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x0000000000536550 in /usr/bin/python3 @@ -33266,13 +33260,13 @@ 197: 50# 0x0000000000628F70 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFF8894229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFFB914229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .[03:10:27] +197: .[23:38:50] 197: 197: **** 197: Range Error @@ -33287,23 +33281,23 @@ 197: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x0000FFFF88162680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x0000FFFFB8962680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFF8673C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFF8673C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFF8673C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFF8673C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x0000FFFF8673C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFFB6F3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFFB6F3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFFB6F3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFFB6F3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x0000FFFFB6F3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 22# 0x0000FFFF8815F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 22# 0x0000FFFFB895F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 23# _PyObject_MakeTpCall in /usr/bin/python3 197: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 25# 0x0000000000536550 in /usr/bin/python3 @@ -33335,13 +33329,13 @@ 197: 51# 0x0000000000628F70 in /usr/bin/python3 197: 52# Py_RunMain in /usr/bin/python3 197: 53# Py_BytesMain in /usr/bin/python3 -197: 54# 0x0000FFFF8894229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 54# 0x0000FFFFB914229C in /lib/aarch64-linux-gnu/libc.so.6 197: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 56# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [03:10:27] +197: [23:38:50] 197: 197: **** 197: Pre-condition Violation @@ -33355,23 +33349,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF88162680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB8962680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFF8673C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFF8673C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFF8673C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFF8673C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFF8673C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFFB6F3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFFB6F3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFFB6F3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFFB6F3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFFB6F3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFF8815F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFFB895F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x0000000000536550 in /usr/bin/python3 @@ -33403,13 +33397,13 @@ 197: 50# 0x0000000000628F70 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFF8894229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFFB914229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [03:10:27] +197: [23:38:50] 197: 197: **** 197: Pre-condition Violation @@ -33423,23 +33417,23 @@ 197: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x0000FFFF88162680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x0000FFFFB8962680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 11# 0x0000FFFF8673C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 12# 0x0000FFFF8673C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 13# 0x0000FFFF8673C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 14# 0x0000FFFF8673C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -197: 15# 0x0000FFFF8673C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 11# 0x0000FFFFB6F3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 12# 0x0000FFFFB6F3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 13# 0x0000FFFFB6F3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 14# 0x0000FFFFB6F3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +197: 15# 0x0000FFFFB6F3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 197: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -197: 21# 0x0000FFFF8815F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +197: 21# 0x0000FFFFB895F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 197: 22# _PyObject_MakeTpCall in /usr/bin/python3 197: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 24# 0x0000000000536550 in /usr/bin/python3 @@ -33471,7 +33465,7 @@ 197: 50# 0x0000000000628F70 in /usr/bin/python3 197: 51# Py_RunMain in /usr/bin/python3 197: 52# Py_BytesMain in /usr/bin/python3 -197: 53# 0x0000FFFF8894229C in /lib/aarch64-linux-gnu/libc.so.6 +197: 53# 0x0000FFFFB914229C in /lib/aarch64-linux-gnu/libc.so.6 197: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 197: 55# _start in /usr/bin/python3 197: ---------- @@ -33479,76 +33473,113 @@ 197: 197: . 197: ---------------------------------------------------------------------- -197: Ran 9 tests in 0.537s +197: Ran 9 tests in 0.471s 197: 197: OK 197: Testing Trajectory wrapper -189/236 Test #197: pyTestTrajectory ....................... Passed 1.32 sec -test 201 - Start 201: pyTestPropertyLists +186: bulk, no symmetry +186/236 Test #197: pyTestTrajectory ....................... Passed 1.00 sec +test 198 + Start 198: pyTestSGroups -201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testPropertyLists.py" -201: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -201: Test timeout computed to be: 1500 +198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testSGroups.py" +198: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +198: Test timeout computed to be: 1500 +195: ....................[23:38:50] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [23:38:50] Explicit valence for atom # 6 F, 2, is greater than permitted +195: [23:38:50] Can't kekulize mol. Unkekulized atoms: 3 4 5 +195: .................[23:38:51] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +198: ............. +198: ---------------------------------------------------------------------- +198: Ran 13 tests in 0.026s +198: +198: OK +198: Testing SubstanceGroups wrapper +187/236 Test #198: pyTestSGroups .......................... Passed 0.48 sec +test 199 + Start 199: pyTestThreads + +199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testThreads.py" +199: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +199: Test timeout computed to be: 1500 +186: [23:38:51] Relabelling existing label +186: Best mapping +188/236 Test #186: testRGroupDecomp ....................... Passed 7.12 sec +test 200 + Start 200: pyTestMultithreadedMolSupplier + +200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" +200: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +200: Test timeout computed to be: 1500 200: .s. 200: ---------------------------------------------------------------------- -200: Ran 3 tests in 0.258s +200: Ran 3 tests in 0.209s 200: 200: OK (skipped=1) 200: Testing Smiles and SD MultithreadedMolSupplier -190/236 Test #200: pyTestMultithreadedMolSupplier ......... Passed 0.71 sec +189/236 Test #200: pyTestMultithreadedMolSupplier ......... Passed 0.55 sec +test 201 + Start 201: pyTestPropertyLists + +201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testPropertyLists.py" +201: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +201: Test timeout computed to be: 1500 +201: [23:38:52] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [23:38:52] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [23:38:52] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +201: .[23:38:52] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [23:38:52] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [23:38:52] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +201: ...[23:38:52] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +201: [23:38:52] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +201: [23:38:52] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +201: . +201: ---------------------------------------------------------------------- +201: Ran 5 tests in 0.016s +201: +201: OK +190/236 Test #201: pyTestPropertyLists .................... Passed 0.47 sec test 202 Start 202: pyCDXMLTest 202: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/test_cdxml.py" 202: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 202: Test timeout computed to be: 1500 -201: [03:10:27] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -201: [03:10:27] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [03:10:27] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: .[03:10:27] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -201: [03:10:27] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [03:10:27] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: ...[03:10:27] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -201: [03:10:27] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -201: [03:10:27] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -201: . -201: ---------------------------------------------------------------------- -201: Ran 5 tests in 0.019s -201: -201: OK -191/236 Test #201: pyTestPropertyLists .................... Passed 0.64 sec +183: [23:38:53] ------------------------------------- +183: [23:38:53] Results do not depend on numThreads (all same) +202: . +202: ---------------------------------------------------------------------- +202: Ran 1 test in 0.011s +202: +202: OK +183: [23:38:53] ------------------------------------- +183: [23:38:53] testTautomerQueries +183: [23:38:53] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +183: [23:38:53] ------------------------------------- +183: [23:38:53] github3881 recursive smarts with rings +191/236 Test #183: substructLibraryTest ................... Passed 11.30 sec test 203 Start 203: molStandardizeTest 203: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest 203: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 203: Test timeout computed to be: 1500 -195: ....................[03:10:28] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [03:10:28] Explicit valence for atom # 6 F, 2, is greater than permitted -195: [03:10:28] Can't kekulize mol. Unkekulized atoms: 3 4 5 -202: . -202: ---------------------------------------------------------------------- -202: Ran 1 test in 0.015s -202: -202: OK -195: .................[03:10:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -192/236 Test #202: pyCDXMLTest ............................ Passed 0.69 sec +192/236 Test #202: pyCDXMLTest ............................ Passed 0.47 sec test 204 Start 204: molNormalizeTest 204: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 204: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 204: Test timeout computed to be: 1500 -204: [03:10:28] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -204: [03:10:28] Initializing Normalizer -204: [03:10:28] Running Normalizer -204: [03:10:28] Rule applied: BrokenazidetoN=N+=N- -204: [03:10:28] Initializing Normalizer -204: [03:10:28] Running Normalizer -204: [03:10:28] Initializing Normalizer -204: [03:10:28] Running Normalizer -193/236 Test #204: molNormalizeTest ....................... Passed 0.41 sec +204: [23:38:53] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +204: [23:38:53] Initializing Normalizer +204: [23:38:53] Running Normalizer +204: [23:38:53] Rule applied: BrokenazidetoN=N+=N- +204: [23:38:53] Initializing Normalizer +204: [23:38:53] Running Normalizer +204: [23:38:53] Initializing Normalizer +204: [23:38:53] Running Normalizer +193/236 Test #204: molNormalizeTest ....................... Passed 0.20 sec test 205 Start 205: molValidateTest @@ -33573,234 +33604,76 @@ 205: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. 205: there 205: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. -194/236 Test #205: molValidateTest ........................ Passed 0.07 sec +194/236 Test #205: molValidateTest ........................ Passed 0.08 sec test 206 Start 206: molChargeTest 206: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest 206: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 206: Test timeout computed to be: 1500 -195/236 Test #206: molChargeTest .......................... Passed 0.28 sec +195/236 Test #206: molChargeTest .......................... Passed 0.13 sec test 207 Start 207: molTautomerTest 207: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 207: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 207: Test timeout computed to be: 1500 -207: [03:10:29] Tautomer enumeration stopped at 292 tautomers: max transforms reached -196/236 Test #203: molStandardizeTest ..................... Passed 2.41 sec +207: [23:38:54] Tautomer enumeration stopped at 292 tautomers: max transforms reached +147: [23:38:54] UFFTYPER: Unrecognized atom type: S_6+6 (0) +147: [23:38:54] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +147: [23:38:54] UFFTYPER: Unrecognized charge state for atom: 0 +196/236 Test #203: molStandardizeTest ..................... Passed 1.45 sec test 208 Start 208: molStandardizeSmallTest 208: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest 208: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 208: Test timeout computed to be: 1500 -197/236 Test #208: molStandardizeSmallTest ................ Passed 0.06 sec +197/236 Test #208: molStandardizeSmallTest ................ Passed 0.05 sec test 209 Start 209: molFragmentTest 209: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 209: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 209: Test timeout computed to be: 1500 -209: [03:10:30] SMARTS Parse Error: syntax error while parsing: [Cl -209: [03:10:30] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -198/236 Test #209: molFragmentTest ........................ Passed 0.08 sec +207: [23:38:54] Tautomer enumeration stopped at 292 tautomers: max transforms reached +209: [23:38:54] SMARTS Parse Error: syntax error while parsing: [Cl +209: [23:38:54] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +198/236 Test #209: molFragmentTest ........................ Passed 0.06 sec test 210 Start 210: molStandardizeCatchTest 210: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 210: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 210: Test timeout computed to be: 1500 -207: [03:10:30] Tautomer enumeration stopped at 292 tautomers: max transforms reached -207: [03:10:30] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -210: Randomness seeded to: 511849313 +207: [23:38:54] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +207: [23:38:55] Tautomer enumeration stopped at 86 tautomers: canceled +207: Enumeration was canceled due to timeout (50 ms) +210: Randomness seeded to: 1277120559 210: * - * - * - * m1 210: * - * - * - * m2 210: * - * - * - * m1 210: * - * - * - * m2 -210: [03:10:30] Can't kekulize mol. Unkekulized atoms: 3 7 -210: [03:10:30] Can't kekulize mol. Unkekulized atoms: 3 8 -210: [03:10:30] Can't kekulize mol. Unkekulized atoms: 2 3 4 -207: [03:10:30] Tautomer enumeration stopped at 35 tautomers: canceled -207: Enumeration was canceled due to timeout (50 ms) -207: 375 -207: Enumeration has completed -207: [03:10:32] Tautomer enumeration stopped at 33 tautomers: canceled -207: CN=c1cc[nH]cn1 -207: CN=c1ccnc[nH]1 -207: CNc1ccncn1 -207: res: CNc1ccncn1 -207: CN=c1cccc[nH]1 -207: CNc1ccccn1 -207: res: CNc1ccccn1 -185: ......[03:10:34] -185: -185: **** -185: Pre-condition Violation -185: RingInfo not initialized -185: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp -185: Failed Expression: df_init -185: ---------- -185: Stacktrace: -185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -185: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -185: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 12# 0x0000FFFFA6ADF530 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 14# 0x0000FFFFA8542680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -185: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -185: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -185: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 20# 0x0000FFFFA6A3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 21# 0x0000FFFFA6A3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x0000FFFFA6A3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x0000FFFFA6A3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x0000FFFFA6A3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -185: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -185: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -185: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -185: 29# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 30# 0x0000FFFFA853F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 31# _PyObject_MakeTpCall in /usr/bin/python3 -185: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 33# 0x0000000000536550 in /usr/bin/python3 -185: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 35# 0x00000000005D32E0 in /usr/bin/python3 -185: 36# 0x00000000006508D4 in /usr/bin/python3 -185: 37# _PyObject_MakeTpCall in /usr/bin/python3 -185: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 39# 0x0000000000536550 in /usr/bin/python3 -185: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 41# 0x00000000005D32E0 in /usr/bin/python3 -185: 42# 0x00000000006508D4 in /usr/bin/python3 -185: 43# _PyObject_MakeTpCall in /usr/bin/python3 -185: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 45# 0x0000000000536550 in /usr/bin/python3 -185: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 47# 0x00000000005D32E0 in /usr/bin/python3 -185: 48# 0x00000000006508D4 in /usr/bin/python3 -185: 49# _PyObject_MakeTpCall in /usr/bin/python3 -185: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 51# 0x0000000000508250 in /usr/bin/python3 -185: 52# _PyObject_MakeTpCall in /usr/bin/python3 -185: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 54# PyEval_EvalCode in /usr/bin/python3 -185: 55# 0x0000000000601BDC in /usr/bin/python3 -185: 56# 0x00000000005FC110 in /usr/bin/python3 -185: 57# 0x0000000000629A90 in /usr/bin/python3 -185: 58# 0x00000000006291D4 in /usr/bin/python3 -185: 59# 0x0000000000628F70 in /usr/bin/python3 -185: 60# Py_RunMain in /usr/bin/python3 -185: 61# Py_BytesMain in /usr/bin/python3 -185: 62# 0x0000FFFFA8F2229C in /lib/aarch64-linux-gnu/libc.so.6 -185: 63# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -185: 64# _start in /usr/bin/python3 -185: ---------- -185: **** -185: -185: [03:10:34] -185: -185: **** -185: Pre-condition Violation -185: RingInfo not initialized -185: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp -185: Failed Expression: df_init -185: ---------- -185: Stacktrace: -185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -185: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 3# 0x0000FFFFA658FCE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -185: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 13# 0x0000FFFFA6ADF530 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 15# 0x0000FFFFA8542680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -185: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -185: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -185: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 21# 0x0000FFFFA6A3C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x0000FFFFA6A3C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x0000FFFFA6A3C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x0000FFFFA6A3C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 25# 0x0000FFFFA6A3C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -185: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -185: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -185: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -185: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so -185: 30# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 31# 0x0000FFFFA853F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -185: 32# _PyObject_MakeTpCall in /usr/bin/python3 -185: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 34# 0x0000000000536550 in /usr/bin/python3 -185: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 36# 0x00000000005D32E0 in /usr/bin/python3 -185: 37# 0x00000000006508D4 in /usr/bin/python3 -185: 38# _PyObject_MakeTpCall in /usr/bin/python3 -185: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 40# 0x0000000000536550 in /usr/bin/python3 -185: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 42# 0x00000000005D32E0 in /usr/bin/python3 -185: 43# 0x00000000006508D4 in /usr/bin/python3 -185: 44# _PyObject_MakeTpCall in /usr/bin/python3 -185: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 46# 0x0000000000536550 in /usr/bin/python3 -185: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 48# 0x00000000005D32E0 in /usr/bin/python3 -185: 49# 0x00000000006508D4 in /usr/bin/python3 -185: 50# _PyObject_MakeTpCall in /usr/bin/python3 -185: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 52# 0x0000000000508250 in /usr/bin/python3 -185: 53# _PyObject_MakeTpCall in /usr/bin/python3 -185: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -185: 55# PyEval_EvalCode in /usr/bin/python3 -185: 56# 0x0000000000601BDC in /usr/bin/python3 -185: 57# 0x00000000005FC110 in /usr/bin/python3 -185: 58# 0x0000000000629A90 in /usr/bin/python3 -185: 59# 0x00000000006291D4 in /usr/bin/python3 -185: 60# 0x0000000000628F70 in /usr/bin/python3 -185: 61# Py_RunMain in /usr/bin/python3 -185: 62# Py_BytesMain in /usr/bin/python3 -185: 63# 0x0000FFFFA8F2229C in /lib/aarch64-linux-gnu/libc.so.6 -185: 64# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -185: 65# _start in /usr/bin/python3 -185: ---------- -185: **** -185: -199/236 Test #207: molTautomerTest ........................ Passed 5.33 sec +210: [23:38:55] Can't kekulize mol. Unkekulized atoms: 3 7 +210: [23:38:55] Can't kekulize mol. Unkekulized atoms: 3 8 +210: [23:38:55] Can't kekulize mol. Unkekulized atoms: 2 3 4 +150: --------------------------------- +150: test getO3AForProbeConfs +150: +150: *********************************************************** +199/236 Test #150: testO3AAlign ........................... Passed 37.38 sec test 211 Start 211: molStandardizePipelineTest 211: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest 211: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 211: Test timeout computed to be: 1500 -211: Randomness seeded to: 3125736536 +211: Randomness seeded to: 638480290 211: 1 Counts line too short: '' on line4 211: 1 Could not instantiate a valid molecule from input 211: 8 Molecule has no atoms -211: [03:10:34] Explicit valence for atom # 1 N, 4, is greater than permitted -211: [03:10:34] Explicit valence for atom # 1 N, 4, is greater than permitted +211: [23:38:55] Explicit valence for atom # 1 N, 4, is greater than permitted +211: [23:38:55] Explicit valence for atom # 1 N, 4, is greater than permitted 211: 8 Explicit valence for atom # 1 N, 4, is greater than permitted 211: 128 An error occurred while preparing the molecule for standardization. 211: 8 The molecule contains an unknown isotope: 3C @@ -33815,13 +33688,13 @@ 211: 4 Bond 3 of dative type is not allowed 211: 4 Enhanced stereochemistry features are not allowed 211: 8 The radical at atom 0 is not allowed -211: [03:10:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +211: [23:38:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 211: 16 The molecule includes non-null Z coordinates 211: 32 Atom 0 too close to bond 2 211: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit 211: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds 211: 64 Atom 0 has adjacent stereo bonds with like orientation -211: [03:10:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +211: [23:38:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 211: 16 The molecule includes non-null Z coordinates 211: 64 Atom 0 has adjacent stereo bonds with like orientation 211: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit @@ -33867,23 +33740,21 @@ 211: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 211: 16777216 The "wavy" style of bond 3 was removed 211: 16777216 The representation of some functional groups was adjusted. -211: [03:10:34] Can't kekulize mol. Unkekulized atoms: 2 3 5 +211: [23:38:55] Can't kekulize mol. Unkekulized atoms: 2 3 5 211: =============================================================================== 211: All tests passed (268 assertions in 5 test cases) 211: -200/236 Test #211: molStandardizePipelineTest ............. Passed 0.50 sec +200/236 Test #211: molStandardizePipelineTest ............. Passed 0.21 sec test 212 Start 212: pyMolStandardize 212: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" 212: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap 212: Test timeout computed to be: 1500 -147: [03:10:35] UFFTYPER: Unrecognized atom type: S_6+6 (0) -147: [03:10:35] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -147: [03:10:35] UFFTYPER: Unrecognized charge state for atom: 0 -212: .....[03:10:36] Tautomer enumeration stopped at 292 tautomers: max transforms reached -212: [03:10:36] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -195: ..[03:10:36] +207: 375 +207: Enumeration has completed +207: [23:38:55] Tautomer enumeration stopped at 66 tautomers: canceled +195: ..[23:38:55] 195: 195: **** 195: Pre-condition Violation @@ -33897,7 +33768,7 @@ 195: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFAF002680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF975A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -33908,17 +33779,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAD53C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAD53C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAD53C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAD53C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAD53C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF95ADC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF95ADC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF95ADC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF95ADC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF95ADC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFAEFFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF9759F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x0000000000536550 in /usr/bin/python3 @@ -33950,13 +33821,13 @@ 195: 55# 0x0000000000628F70 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFAFD4229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF982E229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [03:10:36] +195: [23:38:55] 195: 195: **** 195: Pre-condition Violation @@ -33970,7 +33841,7 @@ 195: 2# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFAF002680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF975A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -33981,17 +33852,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAD53C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAD53C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAD53C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAD53C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAD53C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF95ADC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF95ADC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF95ADC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF95ADC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF95ADC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFAEFFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF9759F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x0000000000536550 in /usr/bin/python3 @@ -34023,13 +33894,13 @@ 195: 55# 0x0000000000628F70 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFAFD4229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF982E229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [03:10:36] +195: [23:38:55] 195: 195: **** 195: Pre-condition Violation @@ -34043,7 +33914,7 @@ 195: 2# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFAF002680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF975A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34054,17 +33925,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAD53C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAD53C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAD53C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAD53C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAD53C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF95ADC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF95ADC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF95ADC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF95ADC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF95ADC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFAEFFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF9759F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x0000000000536550 in /usr/bin/python3 @@ -34096,13 +33967,13 @@ 195: 55# 0x0000000000628F70 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFAFD4229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF982E229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [03:10:36] +195: [23:38:55] 195: 195: **** 195: Pre-condition Violation @@ -34116,7 +33987,7 @@ 195: 2# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFAF002680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF975A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34127,17 +33998,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAD53C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAD53C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAD53C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAD53C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAD53C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF95ADC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF95ADC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF95ADC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF95ADC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF95ADC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFAEFFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF9759F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x0000000000536550 in /usr/bin/python3 @@ -34169,13 +34040,13 @@ 195: 55# 0x0000000000628F70 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFAFD4229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF982E229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: [03:10:36] +195: [23:38:55] 195: 195: **** 195: Pre-condition Violation @@ -34189,7 +34060,7 @@ 195: 2# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFAF002680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF975A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34200,17 +34071,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAD53C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAD53C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAD53C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAD53C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAD53C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF95ADC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF95ADC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF95ADC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF95ADC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF95ADC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFAEFFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF9759F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x0000000000536550 in /usr/bin/python3 @@ -34242,13 +34113,13 @@ 195: 55# 0x0000000000628F70 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFAFD4229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF982E229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: .....[03:10:36] +195: .....[23:38:56] 195: 195: **** 195: Range Error @@ -34262,7 +34133,7 @@ 195: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFAF002680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF975A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34273,17 +34144,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAD53C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAD53C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAD53C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAD53C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAD53C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF95ADC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF95ADC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF95ADC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF95ADC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF95ADC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFAEFFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF9759F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x0000000000536550 in /usr/bin/python3 @@ -34315,49 +34186,49 @@ 195: 55# 0x0000000000628F70 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFAFD4229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF982E229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: ......[03:10:36] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -195: [03:10:36] ERROR: Smiles parse error on line 0 -195: [03:10:36] ERROR: Cannot create molecule from : 'c1ccccc' -195: [03:10:36] SMILES Parse Error: extra open parentheses while parsing: C(C -195: [03:10:36] SMILES Parse Error: check for mistakes around position 2: -195: [03:10:36] C(C -195: [03:10:36] ~^ -195: [03:10:36] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -195: [03:10:36] ERROR: Smiles parse error on line 3 -195: [03:10:36] ERROR: Cannot create molecule from : 'C(C' -195: [03:10:36] Explicit valence for atom # 1 C, 5, is greater than permitted -195: [03:10:36] ERROR: Could not sanitize molecule on line 6 -195: [03:10:36] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -195: [03:10:36] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -195: [03:10:36] ERROR: Smiles parse error on line 0 -195: [03:10:36] ERROR: Cannot create molecule from : 'c1ccccc' -195: [03:10:36] SMILES Parse Error: extra open parentheses while parsing: C(C -195: [03:10:36] SMILES Parse Error: check for mistakes around position 2: -195: [03:10:36] C(C -195: [03:10:36] ~^ -195: [03:10:36] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -195: [03:10:36] ERROR: Smiles parse error on line 3 -195: [03:10:36] ERROR: Cannot create molecule from : 'C(C' -195: [03:10:36] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -195: [03:10:36] ERROR: Smiles parse error on line 6 -195: [03:10:36] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -195: [03:10:36] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [03:10:36] ERROR: Could not sanitize molecule ending on line 21 -195: [03:10:36] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -195: [03:10:36] ERROR: EOF hit while reading atoms -195: [03:10:36] ERROR: moving to the beginning of the next molecule -195: [03:10:36] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [03:10:36] ERROR: Could not sanitize molecule ending on line 21 -195: [03:10:36] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -195: [03:10:36] ERROR: EOF hit while reading atoms -195: [03:10:36] ERROR: moving to the beginning of the next molecule -195: ....[03:10:36] +195: ......[23:38:56] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +195: [23:38:56] ERROR: Smiles parse error on line 0 +195: [23:38:56] ERROR: Cannot create molecule from : 'c1ccccc' +195: [23:38:56] SMILES Parse Error: extra open parentheses while parsing: C(C +195: [23:38:56] SMILES Parse Error: check for mistakes around position 2: +195: [23:38:56] C(C +195: [23:38:56] ~^ +195: [23:38:56] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +195: [23:38:56] ERROR: Smiles parse error on line 3 +195: [23:38:56] ERROR: Cannot create molecule from : 'C(C' +195: [23:38:56] Explicit valence for atom # 1 C, 5, is greater than permitted +195: [23:38:56] ERROR: Could not sanitize molecule on line 6 +195: [23:38:56] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +195: [23:38:56] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +195: [23:38:56] ERROR: Smiles parse error on line 0 +195: [23:38:56] ERROR: Cannot create molecule from : 'c1ccccc' +195: [23:38:56] SMILES Parse Error: extra open parentheses while parsing: C(C +195: [23:38:56] SMILES Parse Error: check for mistakes around position 2: +195: [23:38:56] C(C +195: [23:38:56] ~^ +195: [23:38:56] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +195: [23:38:56] ERROR: Smiles parse error on line 3 +195: [23:38:56] ERROR: Cannot create molecule from : 'C(C' +195: [23:38:56] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +195: [23:38:56] ERROR: Smiles parse error on line 6 +195: [23:38:56] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +195: [23:38:56] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [23:38:56] ERROR: Could not sanitize molecule ending on line 21 +195: [23:38:56] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +195: [23:38:56] ERROR: EOF hit while reading atoms +195: [23:38:56] ERROR: moving to the beginning of the next molecule +195: [23:38:56] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [23:38:56] ERROR: Could not sanitize molecule ending on line 21 +195: [23:38:56] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +195: [23:38:56] ERROR: EOF hit while reading atoms +195: [23:38:56] ERROR: moving to the beginning of the next molecule +195: ....[23:38:56] 195: 195: **** 195: Pre-condition Violation @@ -34371,7 +34242,7 @@ 195: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFAF002680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF975A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34382,17 +34253,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAD53C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAD53C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAD53C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAD53C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAD53C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF95ADC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF95ADC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF95ADC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF95ADC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF95ADC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFAEFFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF9759F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x0000000000536550 in /usr/bin/python3 @@ -34424,13 +34295,13 @@ 195: 55# 0x0000000000628F70 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFAFD4229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF982E229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: .............[03:10:36] +195: .............[23:38:56] 195: 195: **** 195: Range Error @@ -34444,7 +34315,7 @@ 195: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 195: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 5# 0x0000FFFFAF002680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 5# 0x0000FFFF975A2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 195: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34455,17 +34326,17 @@ 195: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 195: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 195: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 16# 0x0000FFFFAD53C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 17# 0x0000FFFFAD53C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 18# 0x0000FFFFAD53C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 19# 0x0000FFFFAD53C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -195: 20# 0x0000FFFFAD53C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 16# 0x0000FFFF95ADC320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 17# 0x0000FFFF95ADC2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 18# 0x0000FFFF95ADC248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 19# 0x0000FFFF95ADC1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +195: 20# 0x0000FFFF95ADC178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 195: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 195: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -195: 26# 0x0000FFFFAEFFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +195: 26# 0x0000FFFF9759F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 195: 27# _PyObject_MakeTpCall in /usr/bin/python3 195: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 195: 29# 0x0000000000536550 in /usr/bin/python3 @@ -34497,241 +34368,241 @@ 195: 55# 0x0000000000628F70 in /usr/bin/python3 195: 56# Py_RunMain in /usr/bin/python3 195: 57# Py_BytesMain in /usr/bin/python3 -195: 58# 0x0000FFFFAFD4229C in /lib/aarch64-linux-gnu/libc.so.6 +195: 58# 0x0000FFFF982E229C in /lib/aarch64-linux-gnu/libc.so.6 195: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 195: 60# _start in /usr/bin/python3 195: ---------- 195: **** 195: -195: ...[03:10:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -195: ............................[03:10:36] SMILES Parse Error: unclosed ring for input: 'C1CC' +195: ...[23:38:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +195: ............................[23:38:56] SMILES Parse Error: unclosed ring for input: 'C1CC' 195: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8| -195: 591 -195: ..[03:10:36] WARNING: not removing hydrogen atom without neighbors -195: [03:10:36] WARNING: not removing hydrogen atom with dummy atom neighbors -195: [03:10:36] WARNING: not removing hydrogen atom with wedged bond -195: [03:10:36] WARNING: not removing hydrogen atom without neighbors -195: [03:10:36] WARNING: not removing hydrogen atom with dummy atom neighbors -212: .[03:10:36] Tautomer enumeration stopped at 35 tautomers: canceled -212: Enumeration was canceled due to timeout (50 ms) -195: ......[03:10:36] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [03:10:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: .[03:10:36] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [03:10:36] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [03:10:36] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [03:10:36] Explicit valence for atom # 1 F, 2, is greater than permitted -195: [03:10:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: [03:10:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: [03:10:36] Can't kekulize mol. Unkekulized atoms: 0 1 2 -195: ..........[03:10:36] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -195: [03:10:36] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -195: .[03:10:36] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -195: [03:10:36] SMILES Parse Error: check for mistakes around position 4: -195: [03:10:36] CCC |$foo;;bar$| ourname -195: [03:10:36] ~~~^ -195: [03:10:36] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -195: ..[03:10:36] SMILES Parse Error: syntax error while parsing: error -195: [03:10:36] SMILES Parse Error: check for mistakes around position 1: -195: [03:10:36] error -195: [03:10:36] ^ -195: [03:10:36] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -195: [03:10:36] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -195: [03:10:36] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -195: [03:10:36] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -195: .........................[03:10:37] SMILES Parse Error: syntax error while parsing: garbage_0 -195: [03:10:37] SMILES Parse Error: check for mistakes around position 1: -195: [03:10:37] garbage_0 -195: [03:10:37] ^ -195: [03:10:37] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -195: [03:10:37] SMILES Parse Error: syntax error while parsing: garbage_2 -195: [03:10:37] SMILES Parse Error: check for mistakes around position 1: -195: [03:10:37] garbage_2 -195: [03:10:37] ^ -195: [03:10:37] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -195: [03:10:37] SMILES Parse Error: syntax error while parsing: garbage_4 -195: [03:10:37] SMILES Parse Error: check for mistakes around position 1: -195: [03:10:37] garbage_4 -195: [03:10:37] ^ -195: [03:10:37] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +195: 643 +195: ..[23:38:56] WARNING: not removing hydrogen atom without neighbors +195: [23:38:56] WARNING: not removing hydrogen atom with dummy atom neighbors +195: [23:38:56] WARNING: not removing hydrogen atom with wedged bond +195: [23:38:56] WARNING: not removing hydrogen atom without neighbors +195: [23:38:56] WARNING: not removing hydrogen atom with dummy atom neighbors +195: ......[23:38:56] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [23:38:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: .[23:38:56] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [23:38:56] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [23:38:56] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [23:38:56] Explicit valence for atom # 1 F, 2, is greater than permitted +195: [23:38:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: [23:38:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 +195: [23:38:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 +212: .....[23:38:56] Tautomer enumeration stopped at 292 tautomers: max transforms reached +195: ..........[23:38:56] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +195: [23:38:56] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +195: .[23:38:56] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +195: [23:38:56] SMILES Parse Error: check for mistakes around position 4: +195: [23:38:56] CCC |$foo;;bar$| ourname +195: [23:38:56] ~~~^ +195: [23:38:56] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +195: ..[23:38:56] SMILES Parse Error: syntax error while parsing: error +195: [23:38:56] SMILES Parse Error: check for mistakes around position 1: +195: [23:38:56] error +195: [23:38:56] ^ +195: [23:38:56] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +195: [23:38:56] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +195: [23:38:56] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +195: [23:38:56] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +212: [23:38:56] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +195: .........................[23:38:56] SMILES Parse Error: syntax error while parsing: garbage_0 +195: [23:38:56] SMILES Parse Error: check for mistakes around position 1: +195: [23:38:56] garbage_0 +195: [23:38:56] ^ +195: [23:38:56] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +195: [23:38:56] SMILES Parse Error: syntax error while parsing: garbage_2 +195: [23:38:56] SMILES Parse Error: check for mistakes around position 1: +195: [23:38:56] garbage_2 +195: [23:38:56] ^ +195: [23:38:56] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +195: [23:38:56] SMILES Parse Error: syntax error while parsing: garbage_4 +195: [23:38:56] SMILES Parse Error: check for mistakes around position 1: +195: [23:38:56] garbage_4 +195: [23:38:56] ^ +195: [23:38:56] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' 195: ............ 195: ---------------------------------------------------------------------- -195: Ran 279 tests in 11.861s +195: Ran 279 tests in 6.823s 195: 195: OK 195: supplier: 195: supplier: 195: supplier: -201/236 Test #195: pyGraphMolWrap ......................... Passed 12.51 sec +201/236 Test #195: pyGraphMolWrap ......................... Passed 7.18 sec test 213 Start 213: testScaffoldNetwork 213: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork 213: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork 213: Test timeout computed to be: 1500 -213: Randomness seeded to: 1014692690 -213: =============================================================================== -213: All tests passed (273 assertions in 19 test cases) -213: -202/236 Test #213: testScaffoldNetwork .................... Passed 2.18 sec +212: .[23:38:56] Tautomer enumeration stopped at 91 tautomers: canceled +212: Enumeration was canceled due to timeout (50 ms) +207: CN=c1cc[nH]cn1 +207: CN=c1ccnc[nH]1 +207: CNc1ccncn1 +207: res: CNc1ccncn1 +207: CN=c1cccc[nH]1 +207: CNc1ccccn1 +207: res: CNc1ccccn1 +202/236 Test #207: molTautomerTest ........................ Passed 2.81 sec test 214 Start 214: pyScaffoldNetwork 214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 214: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 214: Test timeout computed to be: 1500 -212: Enumeration has completed 214: ....... 214: ---------------------------------------------------------------------- -214: Ran 7 tests in 0.050s +214: Ran 7 tests in 0.025s 214: 214: OK -150: --------------------------------- -150: test getO3AForProbeConfs -150: -150: *********************************************************** -203/236 Test #150: testO3AAlign ........................... Passed 49.87 sec +203/236 Test #214: pyScaffoldNetwork ...................... Passed 0.26 sec test 215 Start 215: pyScaffoldNetworkPickling 215: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" 215: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 215: Test timeout computed to be: 1500 -204/236 Test #214: pyScaffoldNetwork ...................... Passed 0.37 sec +215: . +215: ---------------------------------------------------------------------- +215: Ran 1 test in 0.009s +215: +215: OK +204/236 Test #215: pyScaffoldNetworkPickling .............. Passed 0.24 sec test 216 Start 216: testMolEnumerator 216: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 216: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator 216: Test timeout computed to be: 1500 -216: Randomness seeded to: 1200614559 -216: [03:10:39] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +216: Randomness seeded to: 2987494765 +216: [23:38:57] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +212: Enumeration has completed 216: =============================================================================== 216: All tests passed (321 assertions in 16 test cases) 216: -205/236 Test #216: testMolEnumerator ...................... Passed 0.10 sec +205/236 Test #216: testMolEnumerator ...................... Passed 0.06 sec test 217 Start 217: pyMolEnumerator 217: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 217: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 217: Test timeout computed to be: 1500 -212: ..........[03:10:40] Explicit valence for atom # 1 N, 4, is greater than permitted -212: [03:10:40] Explicit valence for atom # 1 N, 4, is greater than permitted -212: [03:10:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -212: [03:10:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: [23:38:57] Tautomer enumeration stopped at 91 tautomers: canceled 217: ... 217: ---------------------------------------------------------------------- -217: Ran 3 tests in 0.021s +217: Ran 3 tests in 0.008s 217: 217: OK -215: . -215: ---------------------------------------------------------------------- -215: Ran 1 test in 0.024s -215: -215: OK -206/236 Test #217: pyMolEnumerator ........................ Passed 0.46 sec +212: ..........[23:38:57] Explicit valence for atom # 1 N, 4, is greater than permitted +212: [23:38:57] Explicit valence for atom # 1 N, 4, is greater than permitted +212: [23:38:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: [23:38:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +206/236 Test #217: pyMolEnumerator ........................ Passed 0.27 sec test 218 Start 218: testAbbreviations 218: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 218: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations 218: Test timeout computed to be: 1500 -207/236 Test #215: pyScaffoldNetworkPickling .............. Passed 0.64 sec +218: Randomness seeded to: 266652303 +218: [23:38:57] SMARTS Parse Error: syntax error while parsing: *fail +218: [23:38:57] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +218: [23:38:57] no suitable SubstanceGroups found +218: =============================================================================== +218: All tests passed (195 assertions in 12 test cases) +218: +207/236 Test #218: testAbbreviations ...................... Passed 0.03 sec test 219 Start 219: pyAbbreviations 219: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 219: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 219: Test timeout computed to be: 1500 -218: Randomness seeded to: 4144431167 -218: [03:10:40] SMARTS Parse Error: syntax error while parsing: *fail -218: [03:10:40] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -218: [03:10:40] no suitable SubstanceGroups found -218: =============================================================================== -218: All tests passed (195 assertions in 12 test cases) -218: -208/236 Test #218: testAbbreviations ...................... Passed 0.06 sec +213: Randomness seeded to: 2457361807 +213: =============================================================================== +213: All tests passed (273 assertions in 19 test cases) +213: +208/236 Test #213: testScaffoldNetwork .................... Passed 1.17 sec test 220 Start 220: generalizedSubstructCatch 220: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 220: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 220: Test timeout computed to be: 1500 -220: Randomness seeded to: 1601012405 -220: =============================================================================== -220: All tests passed (486 assertions in 10 test cases) -220: -209/236 Test #220: generalizedSubstructCatch .............. Passed 0.31 sec +219: ....... +219: ---------------------------------------------------------------------- +219: Ran 7 tests in 0.013s +219: +219: OK +209/236 Test #219: pyAbbreviations ........................ Passed 0.28 sec test 221 Start 221: pyGeneralizedSubstruct 221: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 221: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 221: Test timeout computed to be: 1500 -219: ....... -219: ---------------------------------------------------------------------- -219: Ran 7 tests in 0.036s -219: -219: OK -210/236 Test #219: pyAbbreviations ........................ Passed 0.79 sec +220: Randomness seeded to: 1147070307 +220: =============================================================================== +220: All tests passed (486 assertions in 10 test cases) +220: +210/236 Test #220: generalizedSubstructCatch .............. Passed 0.28 sec test 222 Start 222: testMolProcessing 222: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing 222: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing 222: Test timeout computed to be: 1500 -211/236 Test #199: pyTestThreads .......................... Passed 15.08 sec +221: ....... +221: ---------------------------------------------------------------------- +221: Ran 7 tests in 0.164s +221: +221: OK +211/236 Test #221: pyGeneralizedSubstruct ................. Passed 0.53 sec test 223 Start 223: pyMolProcessing 223: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" 223: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap 223: Test timeout computed to be: 1500 -221: ....... -221: ---------------------------------------------------------------------- -221: Ran 7 tests in 0.218s -221: -221: OK -212/236 Test #221: pyGeneralizedSubstruct ................. Passed 0.77 sec +212: ............[23:38:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212: [23:38:58] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +212: [23:38:58] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +212: ........[23:38:58] Explicit valence for atom # 1 O, 3, is greater than permitted +212: .. +212: ---------------------------------------------------------------------- +212: Ran 38 tests in 2.836s +212: +212: OK +212: done +212/236 Test #212: pyMolStandardize ....................... Passed 3.19 sec test 224 Start 224: testMIF 224: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF 224: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields 224: Test timeout computed to be: 1500 -224: Randomness seeded to: 878832190 +224: Randomness seeded to: 2219649383 224: =============================================================================== 224: All tests passed (27926 assertions in 8 test cases) 224: -213/236 Test #224: testMIF ................................ Passed 0.11 sec +213/236 Test #224: testMIF ................................ Passed 0.08 sec test 225 Start 225: pyMIF 225: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" 225: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap 225: Test timeout computed to be: 1500 -212: ............[03:10:41] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -212: [03:10:41] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -212: [03:10:41] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -212: ........[03:10:42] Explicit valence for atom # 1 O, 3, is greater than permitted -225: ....... -225: ---------------------------------------------------------------------- -225: Ran 7 tests in 0.170s -225: -225: OK -225: Testing MIF wrapper 223: .. 223: ---------------------------------------------------------------------- -223: Ran 2 tests in 0.613s +223: Ran 2 tests in 0.509s 223: 223: OK -212: .. -212: ---------------------------------------------------------------------- -212: Ran 38 tests in 6.731s -212: -212: OK -212: done -214/236 Test #223: pyMolProcessing ........................ Passed 1.08 sec +214/236 Test #223: pyMolProcessing ........................ Passed 0.88 sec test 226 Start 226: testQuery @@ -34771,7 +34642,7 @@ 227: ------------------------------------- 227: ExplicitFeatures 2D, string type. 227: done -216/236 Test #227: testBaseFeatures ....................... Passed 0.02 sec +216/236 Test #227: testBaseFeatures ....................... Passed 0.01 sec test 228 Start 228: testMatCalc @@ -34823,56 +34694,88 @@ 228: 9.49496e+07 228: 2.25618e+08 228: 1.30219e+08 -217/236 Test #228: testMatCalc ............................ Passed 0.01 sec +217/236 Test #228: testMatCalc ............................ Passed 0.02 sec test 229 Start 229: pyMatCalc 229: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 229: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 229: Test timeout computed to be: 1500 -218/236 Test #225: pyMIF .................................. Passed 0.93 sec +225: ....... +225: ---------------------------------------------------------------------- +225: Ran 7 tests in 0.047s +225: +225: OK +225: Testing MIF wrapper +218/236 Test #225: pyMIF .................................. Passed 0.34 sec test 230 Start 230: testSimDivPickers 230: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/testSimDivPickers 230: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers 230: Test timeout computed to be: 1500 -230: [03:10:42] ------------------------------------- -230: [03:10:42] Testing github issue 1421: MaxMinPicker picking non-existent element. -230: [03:10:42] Done -230: [03:10:42] ------------------------------------- -230: [03:10:42] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -230: [03:10:42] Done -219/236 Test #230: testSimDivPickers ...................... Passed 0.01 sec +230: [23:38:59] ------------------------------------- +230: [23:38:59] Testing github issue 1421: MaxMinPicker picking non-existent element. +230: [23:38:59] Done +230: [23:38:59] ------------------------------------- +230: [23:38:59] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +230: [23:38:59] Done +219/236 Test #230: testSimDivPickers ...................... Passed 0.00 sec test 231 Start 231: pickersTestsCatch 231: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 231: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers 231: Test timeout computed to be: 1500 -220/236 Test #212: pyMolStandardize ....................... Passed 7.66 sec +231: Randomness seeded to: 1830758343 +231: =============================================================================== +231: All tests passed (21267 assertions in 1 test case) +231: +220/236 Test #231: pickersTestsCatch ...................... Passed 0.11 sec test 232 Start 232: pySimDivPickers 232: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/Wrap/testPickers.py" 232: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap 232: Test timeout computed to be: 1500 -231: Randomness seeded to: 228973219 -231: =============================================================================== -231: All tests passed (21267 assertions in 1 test case) -231: -221/236 Test #231: pickersTestsCatch ...................... Passed 0.17 sec +232: [23:38:59] the useCache argument is deprecated and ignored +229: ..... +229: ---------------------------------------------------------------------- +229: Ran 5 tests in 0.404s +229: +229: OK +232: ...[23:38:59] the useCache argument is deprecated and ignored +232: [23:38:59] the useCache argument is deprecated and ignored +232: .[23:38:59] the useCache argument is deprecated and ignored +221/236 Test #229: pyMatCalc .............................. Passed 0.78 sec test 233 Start 233: pyRanker 233: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/testRanker.py" 233: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap 233: Test timeout computed to be: 1500 -232: [03:10:42] the useCache argument is deprecated and ignored -232: ...[03:10:42] the useCache argument is deprecated and ignored -232: [03:10:42] the useCache argument is deprecated and ignored -232: .[03:10:42] the useCache argument is deprecated and ignored -233: ..[03:10:43] +222: Randomness seeded to: 3216067639 +222: =============================================================================== +222: All tests passed (203 assertions in 1 test case) +222: +222/236 Test #222: testMolProcessing ...................... Passed 2.29 sec +test 234 + Start 234: testChemicalFeatures + +234: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures +234: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures +234: Test timeout computed to be: 1500 +234: ----------------------------------------- +234: Test1 +234: Done +223/236 Test #234: testChemicalFeatures ................... Passed 0.01 sec +test 235 + Start 235: pyFeatures + +235: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/testFeatures.py" +235: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap +235: Test timeout computed to be: 1500 +233: ..[23:39:00] 233: 233: **** 233: Invariant Violation @@ -34887,14 +34790,14 @@ 233: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 233: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 233: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -233: 6# 0x0000FFFF9EBB2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +233: 6# 0x0000FFFFA8052680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 233: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 233: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 233: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 233: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 233: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so 233: 12# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -233: 13# 0x0000FFFF9EBAF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +233: 13# 0x0000FFFFA804F25C 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# 0x0000000000536550 in /usr/bin/python3 @@ -34926,7 +34829,7 @@ 233: 42# 0x0000000000628F70 in /usr/bin/python3 233: 43# Py_RunMain in /usr/bin/python3 233: 44# Py_BytesMain in /usr/bin/python3 -233: 45# 0x0000FFFFA04D229C in /lib/aarch64-linux-gnu/libc.so.6 +233: 45# 0x0000FFFFA997229C 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: ---------- @@ -34934,32 +34837,10 @@ 233: 233: ... 233: ---------------------------------------------------------------------- -233: Ran 5 tests in 0.049s +233: Ran 5 tests in 0.014s 233: 233: OK -222/236 Test #233: pyRanker ............................... Passed 0.77 sec -test 234 - Start 234: testChemicalFeatures - -234: Test command: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures -234: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures -234: Test timeout computed to be: 1500 -234: ----------------------------------------- -234: Test1 -234: Done -223/236 Test #234: testChemicalFeatures ................... Passed 0.03 sec -test 235 - Start 235: pyFeatures - -235: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/testFeatures.py" -235: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap -235: Test timeout computed to be: 1500 -229: ..... -229: ---------------------------------------------------------------------- -229: Ran 5 tests in 0.703s -229: -229: OK -224/236 Test #229: pyMatCalc .............................. Passed 1.34 sec +224/236 Test #233: pyRanker ............................... Passed 0.26 sec test 236 Start 236: pythonProjectTests @@ -34972,68 +34853,219 @@ 235: 235: OK 235: Testing ChemicalFeatures Wrapper code: -225/236 Test #235: pyFeatures ............................. Passed 0.68 sec -222: Randomness seeded to: 916208833 -222: =============================================================================== -222: All tests passed (203 assertions in 1 test case) -222: -226/236 Test #222: testMolProcessing ...................... Passed 3.06 sec -232: ....... -232: ---------------------------------------------------------------------- -232: Ran 11 tests in 1.546s -232: -232: OK -227/236 Test #232: pySimDivPickers ........................ Passed 1.83 sec +185: ......[23:39:00] +185: +185: **** +185: Pre-condition Violation +185: RingInfo not initialized +185: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp +185: Failed Expression: df_init +185: ---------- +185: Stacktrace: +185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +185: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +185: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 12# 0x0000FFFF968FF530 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 14# 0x0000FFFF98362680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +185: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +185: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +185: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 20# 0x0000FFFF9685C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 21# 0x0000FFFF9685C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x0000FFFF9685C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x0000FFFF9685C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x0000FFFF9685C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +185: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +185: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +185: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +185: 29# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 30# 0x0000FFFF9835F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 31# _PyObject_MakeTpCall in /usr/bin/python3 +185: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 33# 0x0000000000536550 in /usr/bin/python3 +185: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 35# 0x00000000005D32E0 in /usr/bin/python3 +185: 36# 0x00000000006508D4 in /usr/bin/python3 +185: 37# _PyObject_MakeTpCall in /usr/bin/python3 +185: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 39# 0x0000000000536550 in /usr/bin/python3 +185: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 41# 0x00000000005D32E0 in /usr/bin/python3 +185: 42# 0x00000000006508D4 in /usr/bin/python3 +185: 43# _PyObject_MakeTpCall in /usr/bin/python3 +185: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 45# 0x0000000000536550 in /usr/bin/python3 +185: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 47# 0x00000000005D32E0 in /usr/bin/python3 +185: 48# 0x00000000006508D4 in /usr/bin/python3 +185: 49# _PyObject_MakeTpCall in /usr/bin/python3 +185: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 51# 0x0000000000508250 in /usr/bin/python3 +185: 52# _PyObject_MakeTpCall in /usr/bin/python3 +185: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 54# PyEval_EvalCode in /usr/bin/python3 +185: 55# 0x0000000000601BDC in /usr/bin/python3 +185: 56# 0x00000000005FC110 in /usr/bin/python3 +185: 57# 0x0000000000629A90 in /usr/bin/python3 +185: 58# 0x00000000006291D4 in /usr/bin/python3 +185: 59# 0x0000000000628F70 in /usr/bin/python3 +185: 60# Py_RunMain in /usr/bin/python3 +185: 61# Py_BytesMain in /usr/bin/python3 +185: 62# 0x0000FFFF98D4229C in /lib/aarch64-linux-gnu/libc.so.6 +185: 63# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +185: 64# _start in /usr/bin/python3 +185: ---------- +185: **** +185: +185: [23:39:00] +185: +185: **** +185: Pre-condition Violation +185: RingInfo not initialized +185: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp +185: Failed Expression: df_init +185: ---------- +185: Stacktrace: +185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +185: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 3# 0x0000FFFF963AFCE8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +185: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 13# 0x0000FFFF968FF530 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 15# 0x0000FFFF98362680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +185: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +185: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +185: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 21# 0x0000FFFF9685C320 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x0000FFFF9685C2B8 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x0000FFFF9685C248 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x0000FFFF9685C1E0 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 25# 0x0000FFFF9685C178 in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +185: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +185: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +185: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +185: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu/rdkit/rdBase.so +185: 30# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 31# 0x0000FFFF9835F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +185: 32# _PyObject_MakeTpCall in /usr/bin/python3 +185: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 34# 0x0000000000536550 in /usr/bin/python3 +185: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 36# 0x00000000005D32E0 in /usr/bin/python3 +185: 37# 0x00000000006508D4 in /usr/bin/python3 +185: 38# _PyObject_MakeTpCall in /usr/bin/python3 +185: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 40# 0x0000000000536550 in /usr/bin/python3 +185: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 42# 0x00000000005D32E0 in /usr/bin/python3 +185: 43# 0x00000000006508D4 in /usr/bin/python3 +185: 44# _PyObject_MakeTpCall in /usr/bin/python3 +185: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 46# 0x0000000000536550 in /usr/bin/python3 +185: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 48# 0x00000000005D32E0 in /usr/bin/python3 +185: 49# 0x00000000006508D4 in /usr/bin/python3 +185: 50# _PyObject_MakeTpCall in /usr/bin/python3 +185: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 52# 0x0000000000508250 in /usr/bin/python3 +185: 53# _PyObject_MakeTpCall in /usr/bin/python3 +185: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +185: 55# PyEval_EvalCode in /usr/bin/python3 +185: 56# 0x0000000000601BDC in /usr/bin/python3 +185: 57# 0x00000000005FC110 in /usr/bin/python3 +185: 58# 0x0000000000629A90 in /usr/bin/python3 +185: 59# 0x00000000006291D4 in /usr/bin/python3 +185: 60# 0x0000000000628F70 in /usr/bin/python3 +185: 61# Py_RunMain in /usr/bin/python3 +185: 62# Py_BytesMain in /usr/bin/python3 +185: 63# 0x0000FFFF98D4229C in /lib/aarch64-linux-gnu/libc.so.6 +185: 64# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +185: 65# _start in /usr/bin/python3 +185: ---------- +185: **** +185: +225/236 Test #235: pyFeatures ............................. Passed 0.44 sec 236: ============================= test session starts ============================== 236: platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 236: rootdir: /build/reproducible-path/rdkit-202503.1/Projects 236: configfile: pytest.ini 236: collected 12 items 236: -185: ............. -185: ---------------------------------------------------------------------- -185: Ran 19 tests in 36.276s -185: -185: OK -185: Testing atom rings -185: testing bond rings -185: searching atom rings -185: searching bond rings -185: done -228/236 Test #185: pySubstructLibrary ..................... Passed 36.98 sec -146: [03:10:52] done -146: [03:10:52] --------------------------------- -146: [03:10:52] test github issue 256: handling of zero-atom molecules +232: ....... +232: ---------------------------------------------------------------------- +232: Ran 11 tests in 1.344s +232: +232: OK +226/236 Test #232: pySimDivPickers ........................ Passed 1.69 sec +227/236 Test #199: pyTestThreads .......................... Passed 12.16 sec +146: [23:39:04] done +146: [23:39:04] --------------------------------- +146: [23:39:04] test github issue 256: handling of zero-atom molecules 146: -146: [03:10:52] --------------------------------- -146: [03:10:52] test embedder callback function -146: [03:10:52] --------------------------------- -146: [03:10:52] test multi-threaded multi-conf embedding +146: [23:39:04] --------------------------------- +146: [23:39:04] test embedder callback function +146: [23:39:04] --------------------------------- +146: [23:39:04] test multi-threaded multi-conf embedding 146: -146: [03:10:55] --------------------------------- -146: [03:10:55] test github issue 563: Incorrect ring stereochemistry after embedding +146: [23:39:06] --------------------------------- +146: [23:39:06] test github issue 563: Incorrect ring stereochemistry after embedding 146: 146: CNC[C@H]1CC[C@H](C[NH3+])CC1 -146: [03:10:57] --------------------------------- -146: [03:10:57] test github issue 568: Incorrect stereochemistry after embedding +146: [23:39:07] --------------------------------- +146: [23:39:07] 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 -210: [03:10:59] Explicit valence for atom # 0 Br, 1, is greater than permitted -210: =============================================================================== -210: All tests passed (38344 assertions in 51 test cases) -210: -229/236 Test #210: molStandardizeCatchTest ................ Passed 29.47 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 +210: [23:39:08] Explicit valence for atom # 0 Br, 1, is greater than permitted +210: =============================================================================== +210: All tests passed (38344 assertions in 51 test cases) +210: +228/236 Test #210: molStandardizeCatchTest ................ Passed 13.93 sec 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]21 146: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 +185: ............. +185: ---------------------------------------------------------------------- +185: Ran 19 tests in 26.834s +185: +185: OK +185: Testing atom rings +185: testing bond rings +185: searching atom rings +185: searching bond rings +185: done +229/236 Test #185: pySubstructLibrary ..................... Passed 27.42 sec 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 146: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 @@ -35041,10 +35073,14 @@ 146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O 146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 146: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 +171: =============================================================================== +171: All tests passed (93 assertions in 5 test cases) +171: +230/236 Test #171: testRascalCluster ...................... Passed 49.69 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 -147: [03:11:12] Interrupted, cancelling conformer generation +147: [23:39:18] Interrupted, cancelling conformer generation 147: Atoms: 147: 0 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: SP3 chi: CCW nbrs:[9 3 1 6] 147: 1 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: SP3 chi: CCW nbrs:[0 13 6 7] @@ -35077,11 +35113,11 @@ 147: 13 7->5 order: 1 147: 14 8->12 order: a conj?: 1 aromatic?: 1 147: 15 11->2 order: 1 stereo: CCW bonds: (9 4 5) conj?: 1 +146: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 147: =============================================================================== 147: All tests passed (12742 assertions in 21 test cases) 147: -230/236 Test #147: distGeomHelpersCatch ................... Passed 85.93 sec -146: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 +231/236 Test #147: distGeomHelpersCatch ................... Passed 62.70 sec 146: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 146: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 146: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 @@ -35095,62 +35131,58 @@ 236: decBase = declarative_base() 236: 236: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -236: ======================== 12 passed, 1 warning in 34.45s ======================== -231/236 Test #236: pythonProjectTests ..................... Passed 35.44 sec -146: [03:11:24] Molecule does not have explicit Hs. Consider calling AddHs() -146: [03:11:17] --------------------------------- -146: [03:11:17] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system -146: [03:11:17] --------------------------------- -146: [03:11:17] More ChEMBL molecules failing bounds smoothing. -146: [03:11:17] --------------------------------- -146: [03:11:17] ugly conformations can be generated for highly constrained ring systems. -146: [03:11:17] --------------------------------- -146: [03:11:17] test embed parameters structure. -146: [03:11:17] --------------------------------- -146: [03:11:17] test github 1227: Hs being used in RMSD filtering. -146: [03:11:17] --------------------------------- -146: [03:11:17] Failure to embed larger aromatic rings. -146: [03:11:20] --------------------------------- -146: [03:11:20] Deterministic with large random seeds -146: [03:11:22] --------------------------------- -146: [03:11:22] Github #1990: seg fault after RemoveHs -146: [03:11:23] --------------------------------- -146: [03:11:23] Github #2246: Use coordMap when starting embedding from random coords -146: [03:11:24] --------------------------------- -146: [03:11:24] Providing a distance bounds matrix. -146: [03:11:24] --------------------------------- -146: [03:11:24] Disabling fragmentation. -146: [03:11:24] --------------------------------- -146: [03:11:24] Using symmetry in conformation pruning. -146: [03:11:24] --------------------------------- -146: [03:11:24] Force trans amides. -146: [03:11:24] --------------------------------- -146: [03:11:24] test missing Hs warning. -146: [03:11:24] --------------------------------- -146: [03:11:24] basic H bond support. -146: [03:11:24] ******************************************************* -232/236 Test #146: testDistGeomHelpers .................... Passed 98.10 sec -171: =============================================================================== -171: All tests passed (93 assertions in 5 test cases) -171: -233/236 Test #171: testRascalCluster ...................... Passed 87.25 sec +236: ======================== 12 passed, 1 warning in 21.55s ======================== +232/236 Test #236: pythonProjectTests ..................... Passed 22.25 sec +146: [23:39:25] Molecule does not have explicit Hs. Consider calling AddHs() +146: [23:39:21] --------------------------------- +146: [23:39:21] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system +146: [23:39:21] --------------------------------- +146: [23:39:21] More ChEMBL molecules failing bounds smoothing. +146: [23:39:21] --------------------------------- +146: [23:39:21] ugly conformations can be generated for highly constrained ring systems. +146: [23:39:21] --------------------------------- +146: [23:39:21] test embed parameters structure. +146: [23:39:21] --------------------------------- +146: [23:39:21] test github 1227: Hs being used in RMSD filtering. +146: [23:39:21] --------------------------------- +146: [23:39:21] Failure to embed larger aromatic rings. +146: [23:39:22] --------------------------------- +146: [23:39:22] Deterministic with large random seeds +146: [23:39:24] --------------------------------- +146: [23:39:24] Github #1990: seg fault after RemoveHs +146: [23:39:24] --------------------------------- +146: [23:39:24] Github #2246: Use coordMap when starting embedding from random coords +146: [23:39:25] --------------------------------- +146: [23:39:25] Providing a distance bounds matrix. +146: [23:39:25] --------------------------------- +146: [23:39:25] Disabling fragmentation. +146: [23:39:25] --------------------------------- +146: [23:39:25] Using symmetry in conformation pruning. +146: [23:39:25] --------------------------------- +146: [23:39:25] Force trans amides. +146: [23:39:25] --------------------------------- +146: [23:39:25] test missing Hs warning. +146: [23:39:25] --------------------------------- +146: [23:39:25] basic H bond support. +146: [23:39:25] ******************************************************* +233/236 Test #146: testDistGeomHelpers .................... Passed 70.04 sec 170: =============================================================================== 170: All tests passed (3590 assertions in 35 test cases) 170: -234/236 Test #170: testRascalMCES ......................... Passed 99.52 sec -174: Randomness seeded to: 2776899196 +234/236 Test #170: testRascalMCES ......................... Passed 60.98 sec +5: [23:39:49] Finished: testMultipleTimes() +5: [23:39:49] +5: ----------------------------------------- +235/236 Test #5: testConcurrentQueue .................... Passed 106.67 sec +174: Randomness seeded to: 2776744936 174: =============================================================================== 174: All tests passed (28 assertions in 2 test cases) 174: -235/236 Test #174: testSynthonSpaceRascalSearch ........... Passed 126.03 sec -5: [03:34:05] Finished: testMultipleTimes() -5: [03:34:05] -5: ----------------------------------------- -236/236 Test #5: testConcurrentQueue .................... Passed 1471.60 sec +236/236 Test #174: testSynthonSpaceRascalSearch ........... Passed 80.32 sec 100% tests passed, 0 tests failed out of 236 -Total Test time (real) = 1471.69 sec +Total Test time (real) = 108.11 sec make[2]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-aarch64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' create-stamp debian/debhelper-build-stamp @@ -37805,37 +37837,37 @@ diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged -dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol MemoryContextAlloc: 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 errstart_cold: 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.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake -dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined +dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202503.1-2_all.deb'. -dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202503.1-2_arm64.deb'. +dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202503.1-2_arm64.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202503.1-2_arm64.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202503.1-2_all.deb'. -dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202503.1-2_arm64.deb'. +dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202503.1-2_arm64.deb'. dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202503.1-2_arm64.deb'. dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202503.1-2_arm64.deb'. -dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202503.1-2_arm64.deb'. dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202503.1-2_arm64.deb'. +dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202503.1-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202503.1-2_arm64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202503.1-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -37843,12 +37875,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/4102197/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4102197/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/2170739 and its subdirectories -I: Current time: Tue May 12 03:38:25 -12 2026 -I: pbuilder-time-stamp: 1778600305 +I: removing directory /srv/workspace/pbuilder/4102197 and its subdirectories +I: Current time: Wed Apr 9 23:44:28 +14 2025 +I: pbuilder-time-stamp: 1744191868