Diff of the two buildlogs: -- --- b1/build.log 2025-03-12 17:48:45.853589080 +0000 +++ b2/build.log 2025-03-12 19:45:48.613178346 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 14 11:29:39 -12 2026 -I: pbuilder-time-stamp: 1776209379 +I: Current time: Thu Mar 13 07:48:51 +14 2025 +I: pbuilder-time-stamp: 1741801731 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -35,52 +35,84 @@ dpkg-source: info: applying disable_riscv64_timeout_tests.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3959858/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/423878/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +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 Mar 12 17:49 /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/423878/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/423878/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='e4cef12a0b8a4afeabfb12b52cafa73c' - 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='3959858' - PS1='# ' - PS2='> ' + INVOCATION_ID=e682fee510c844feb9c2b252e6f8a6d4 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=423878 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.UNOoVF5j/pbuilderrc_sfEh --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UNOoVF5j/b1 --logfile b1/build.log rdkit_202409.6-2.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.UNOoVF5j/pbuilderrc_9sya --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UNOoVF5j/b2 --logfile b2/build.log rdkit_202409.6-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3959858/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/423878/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -582,7 +614,7 @@ Get: 377 http://deb.debian.org/debian trixie/main amd64 texlive-latex-recommended all 2024.20250114-1 [8760 kB] Get: 378 http://deb.debian.org/debian trixie/main amd64 texlive-pictures all 2024.20250114-1 [17.1 MB] Get: 379 http://deb.debian.org/debian trixie/main amd64 texlive-latex-extra all 2024.20250114-1 [24.7 MB] -Fetched 420 MB in 16s (25.5 MB/s) +Fetched 420 MB in 31s (13.5 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 ... 19800 files and directories currently installed.) @@ -1798,8 +1830,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Apr 14 23:34:15 UTC 2026. -Universal Time is now: Tue Apr 14 23:34:15 UTC 2026. +Local time is now: Wed Mar 12 17:59:16 UTC 2025. +Universal Time is now: Wed Mar 12 17:59:16 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-4.1) ... @@ -2193,7 +2225,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202409.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rdkit_202409.6-2_source.changes +I: user script /srv/workspace/pbuilder/423878/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/423878/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202409.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rdkit_202409.6-2_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202409.6-2 dpkg-buildpackage: info: source distribution unstable @@ -2317,8 +2353,8 @@ command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (7.7s) --- Generating done (2.3s) +-- Configuring done (17.3s) +-- Generating done (12.8s) CMake Warning: Manually-specified variables were not used by the project: @@ -2379,110 +2415,110 @@ command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (3.3s) +-- Configuring done (5.0s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17 make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6' dh_auto_build - cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202409.6 -B/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/CMakeFiles 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/build/reproducible-path/rdkit-202409.6/External/GA/ga/BinaryStringChromosomePolicy.cpp cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/RDGeneral/versions.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /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 -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD 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External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -MF CMakeFiles/ga.dir/util/Util.cpp.o.d -o CMakeFiles/ga.dir/util/Util.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/util/Util.cpp [ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/External/GA/ga/BinaryStringChromosomePolicy.cpp +[ 1%] Built target coordgen_support cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/External/GA/util/RandomUtil.cpp -[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -[ 1%] Built target inchi_support -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -MF CMakeFiles/ga.dir/util/Util.cpp.o.d -o CMakeFiles/ga.dir/util/Util.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/util/Util.cpp +[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -MF CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o.d -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/LocaleSwitcher.cpp [ 1%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 @@ -2493,207 +2529,214 @@ cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/ga.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2024.09.6 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o CMakeFiles/ga.dir/util/Util.cpp.o /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2024.09.6 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 2%] Built target ga [ 2%] Linking CXX static library librdkitCatch.a cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 2%] Built target ga /usr/bin/ar qc librdkitCatch.a CMakeFiles/rdkitCatch.dir/catch_main.cpp.o /usr/bin/ranlib librdkitCatch.a make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 2%] Built target rdkitCatch [ 2%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 -[ 2%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDStreams.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2024.09.6 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 2%] Built target RDStreams +[ 2%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/RDGeneral.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2024.09.6 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeneral.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1 ../../lib/libRDKitRDGeneral.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 2%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake "--color=" make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDBoost /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake "--color=" make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake "--color=" make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDBoost /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake "--color=" +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake "--color=" -make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Query /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Query /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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-DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -MF CMakeFiles/DataStructs.dir/BitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitVect.cpp cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -MF CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o.d -o CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/catch_logs.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Query && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o -MF CMakeFiles/testMatrices.dir/testMatrices.cpp.o.d -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/testMatrices.cpp +[ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o -MF CMakeFiles/DataStructs.dir/BitOps.cpp.o.d -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitOps.cpp +[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF 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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 -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/RealValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/RealValueVect.cpp -[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Utils.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -[ 4%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogParams.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Catalogs/CatalogParams.cpp -[ 4%] Linking CXX executable testConcurrentQueue -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConcurrentQueue.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o +[ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -MF CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o.d -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/testPickers.cpp -[ 7%] Linking CXX shared library ../../lib/libRDKitCatalogs.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/Catalogs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2024.09.6 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 7%] Built target Catalogs -[ 7%] Linking CXX executable testMatrices -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMatrices.dir/link.d CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 7%] Built target testMatrices -[ 8%] Linking CXX executable logTestsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/logTestsCatch.dir/link.d CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 8%] Built target logTestsCatch +[ 8%] Linking CXX executable dictTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 [ 8%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 +[ 8%] Linking CXX executable testQuery +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dictTestsCatch.dir/link.d CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 8%] Built target dictTestsCatch /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2024.09.6 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o CMakeFiles/DataStructs.dir/RealValueVect.cpp.o ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' @@ -2702,83 +2745,71 @@ make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake "--color=" +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testQuery.dir/link.d CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend -make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.dir/depend +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake "--color=" +make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.dir/depend make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend -make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/InfoTheory /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake "--color=" +make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/catchDataStructs.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/point.cpp.o -MF CMakeFiles/RDGeometryLib.dir/point.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/point.cpp -[ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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+cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pickersTestsCatch.dir/link.d CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSimDivPickers.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKithc.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 12%] Built target RDGeometryLib -make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend -make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend -make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend -make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend -make -f Code/Geometry/CMakeFiles/testRealValueGrid.dir/build.make Code/Geometry/CMakeFiles/testRealValueGrid.dir/depend -make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol 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directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Geometry 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/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_BitOps.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 14%] Built target InfoTheory +make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 14%] Built target testDict make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures 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/build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/FreeChemicalFeature.cpp +[ 14%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 +[ 14%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMetricMatrixCalc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/AlignPoints.cpp +[ 14%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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library ../../../lib/libRDKitAlignment.so +make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 14%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -MF CMakeFiles/rdGeometry.dir/Point.cpp.o.d -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/Point.cpp +[ 14%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt 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Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/UniformGrid3D.cpp +[ 15%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o -MF CMakeFiles/cQuantize.dir/cQuantize.cpp.o.d -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ML/Data/cQuantize.cpp -[ 16%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script 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/build/reproducible-path/rdkit-202409.6/Code/Numerics /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 15%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/testConrec.cpp +[ 15%] Linking CXX executable testTransforms +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake "--color=" -[ 16%] Built target geometryTestsCatch -/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': -/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FindRings.cpp:1292:36: warning: unused parameter 'mol' [-Wunused-parameter] - 1292 | void findRingFamilies(const ROMol &mol) { - | ~~~~~~~~~~~~~^~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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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-[ 17%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o +[ 16%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o -MF CMakeFiles/testAlignment.dir/testAlignment.cpp.o.d -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/testAlignment.cpp -[ 17%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/Clustering.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 17%] Linking CXX executable testFPB -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script 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+/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': +/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FindRings.cpp:1292:36: warning: unused parameter 'mol' [-Wunused-parameter] + 1292 | void findRingFamilies(const ROMol &mol) { + | ~~~~~~~~~~~~~^~~ +[ 18%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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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../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 19%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 19%] Built target testConrec +[ 19%] Built target rdGeometry [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Resonance.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o @@ -3133,61 +3209,21 @@ cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 20%] Built target rdInfoTheory -[ 20%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdAlignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 20%] Built target rdAlignment -[ 20%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 -/usr/bin/c++ 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 20%] Built target rdGeometry -[ 20%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/cDataStructs.dir/link.d 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 20%] Built target cDataStructs [ 20%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/GraphMol.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2024.09.6 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o CMakeFiles/GraphMol.dir/Resonance.cpp.o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o CMakeFiles/GraphMol.dir/new_canon.cpp.o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o CMakeFiles/GraphMol.dir/FindStereo.cpp.o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o CMakeFiles/GraphMol.dir/Atropisomers.cpp.o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o CMakeFiles/GraphMol.dir/MolProps.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -3202,375 +3238,430 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -MF CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o.d -o CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GenericGroups/GenericGroups.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake "--color=" +[ 21%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend -make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend -make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Trajectory/Trajectory.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake "--color=" +[ 21%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -MF CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o.d -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/MolTransforms.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -MF CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o.d -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/Subgraphs.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -MF 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SmilesParse/SmilesParseOps.cpp +make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make 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+cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/Digraph.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp -[ 26%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -cd 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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-202409.6/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp -[ 27%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so +[ 23%] Built target tableTestsCatch +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Configuration.cpp +[ 24%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o +cd 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-Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalogParams.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmartsWrite.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 24%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 +[ 24%] Linking CXX shared module ../../../rdkit/rdBase.so +cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp +[ 24%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2024.09.6 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 27%] Built target MolCatalog +[ 24%] Built target MolCatalog make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 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-DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -MF CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o.d -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp -[ 27%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 -[ 27%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 +[ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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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../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so +[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/Trajectory.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -MF CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o.d -o CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.cpp +[ 24%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/PartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build +[ 24%] Built target PartialCharges +make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 28%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/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 -DrdCIPLabeler_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp -[ 28%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 24%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp +[ 24%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/Numerics/Optimizer/LinearSearch.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Rule2.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule2.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule3.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Rule4a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp +[ 25%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 +[ 25%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GenericGroups.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 28%] Built target GenericGroups +[ 25%] Built target GenericGroups make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 29%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -[ 29%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o +[ 25%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Substruct/SubstructMatch.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructUtils.cpp -[ 29%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o +cd 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-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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp +[ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SmilesParse/smarts.tab.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 25%] Built target MolTransforms +make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 25%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK 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Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -MF CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o.d -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp +[ 25%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Optimizer.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2024.09.6 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 29%] Built target Optimizer +[ 25%] Built target Optimizer +make -f 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 25%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNAttribs.cpp make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend -make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend make[4]: Entering directory 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer/testOptimizer.cpp +[ 25%] Building CXX object 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructUtils.cpp +[ 26%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so +cd 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/usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rdTrajectory.cpp +[ 30%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 30%] Built target rdMolCatalog +make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake 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Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.cpp +[ 30%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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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-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/MMFF/Params.cpp -[ 31%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 -[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 32%] Built target rdCIPLabeler +[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ 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../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 32%] Built target rdPartialCharges -[ 32%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolTransforms.dir/link.d 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/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SubstructMatch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 32%] Built target SubstructMatch [ 32%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 -[ 32%] Built target MolTransforms -make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && 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-I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -MF CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o.d -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp -[ 32%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && 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Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp -[ 32%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' @@ -3583,514 +3674,571 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 32%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/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 -DrdSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -MF CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o.d -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp -[ 32%] Linking CXX executable testOptimizer -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 32%] Built target rdtrajectory -[ 32%] Linking CXX shared module ../../../rdkit/rdBase.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 -[ 32%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 32%] Built target rdqueries -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ShapeHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2024.09.6 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2024.09.6 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 32%] Built target ShapeHelpers -make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -MF CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o.d -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp -[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 32%] Built target rdMolCatalog -[ 33%] Linking CXX shared library ../../lib/libRDKitForceField.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 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 CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 33%] Built target ForceField -[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 -[ 33%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 33%] Built target rdSLNParse -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInterchange.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 33%] 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-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/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 -DrdMolInterchange_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp -[ 33%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so +[ 32%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 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 CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 33%] Built target SmilesParse +[ 32%] Built target SmilesParse +make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.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[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/depend -make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.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-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/depend +make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend +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-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/queryTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend -make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/depend -make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build +make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/depend +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-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build +make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 32%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/depend +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -MF CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o.d -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/AlignMolecules.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build +make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 32%] Building CXX object Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/queryTestsCatch.dir/catch_queries.cpp.o -MF CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o.d -o CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_queries.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make[4]: Leaving directory 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CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so +[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script 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/usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 34%] Built target SubstructMatch -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/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend -make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend -make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend -make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend -make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend +[ 33%] Built target rdShapeHelpers make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make 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/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build +make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 33%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +[ 34%] Linking CXX shared library ../../lib/libRDKitForceField.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 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 CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build -make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 34%] Built target ForceField +make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make 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-I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -MF CMakeFiles/testPartialCharges.dir/test1.cpp.o.d -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/test1.cpp +[ 34%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 37%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganFingerprints.cpp +[ 35%] Linking CXX executable v2smiTestCatch +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2smiTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2smiTestCatch.dir/link.d CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o -o v2smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 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/usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 37%] Built target molbundleTestsCatch +[ 35%] Built target molbundleTestsCatch +[ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp +[ 36%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 +[ 36%] Linking CXX executable testSubgraphs1 +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs1.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared 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graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 38%] Built target graphmolqueryTest +make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2024.09.6 ../../../lib/libRDKitFragCatalog.so.1 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.cpp +[ 40%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatParams.cpp +[ 40%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 38%] Built target FragCatalog -[ 38%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/Abbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2024.09.6 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2024.09.6 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so +[ 40%] Built target rdReducedGraphs +[ 40%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragFPGenerator.cpp +[ 40%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdCoordGen.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 38%] Built target Abbreviations -make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake "--color=" +[ 40%] Built target rdCoordGen +[ 40%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 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.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build +[ 40%] Built target Fingerprints +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend +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-202409.6/obj-x86_64-linux-gnu' -[ 38%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/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 -DrdAbbreviations_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp -[ 38%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2024.09.6 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 38%] Built target MolAlign -make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend -make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp +[ 40%] Linking CXX executable testSLNParse +cd 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 40%] Built target FilterCatalog +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-202409.6/obj-x86_64-linux-gnu' -[ 39%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/EmbeddedFrag.cpp.o -MF CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o.d -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/EmbeddedFrag.cpp -[ 40%] Linking CXX executable testReducedGraphs -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 40%] Built target testReducedGraphs +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake "--color=" [ 40%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 41%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp +[ 41%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 +[ 41%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Depictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared 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Built target rdAbbreviations +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FragCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2024.09.6 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o 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+make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 41%] Built target Depictor +make -f External/INCHI-API/CMakeFiles/RDInchiLib.dir/build.make External/INCHI-API/CMakeFiles/RDInchiLib.dir/depend +make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so +make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend +[ 41%] Built target FragCatalog +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/INCHI-API /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API 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Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 41%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/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 -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -MF CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o.d -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 40%] Built target ForceFieldHelpers +make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build +[ 41%] Building CXX object External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDInchiLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDINCHILIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms/MolFragmenter.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 41%] Built target ForceFieldHelpers make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/depend make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ForceField /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/DependInfo.cmake "--color=" +[ 41%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o +[ 41%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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/build/reproducible-path/rdkit-202409.6/Code/ForceField/catch_tests.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -MF CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/normalize.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build make[4]: Entering directory 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralViolationContrib.cpp -[ 41%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -cd 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -MF CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o.d -o CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.cpp -[ 41%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 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.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 41%] Built target FilterCatalog -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-202409.6/obj-x86_64-linux-gnu' -cd 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/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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/usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 42%] Built target rdReducedGraphs -[ 42%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 42%] Built target Fingerprints -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend -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-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 42%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp -[ 42%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp [ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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-Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2024.09.6 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 42%] Built target DistGeometry +[ 43%] Built target DistGeometry make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend make[4]: Entering directory 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/testDistGeom.cpp +[ 43%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o +[ 43%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o cd 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/Wrap/DistGeom.cpp -[ 43%] Linking CXX executable ForceFieldsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldsCatch.dir/link.txt --verbose=1 -[ 43%] Linking CXX executable testSLNParse -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 +[ 43%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o +cd 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Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/testDistGeom.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ForceFieldsCatch.dir/link.d CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -o ForceFieldsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 43%] Built target ForceFieldsCatch -/usr/bin/c++ -g -O2 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Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 43%] Built target testSLNParse -[ 43%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdCoordGen.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/x86_64-linux-gnu/libcoordgen.so 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executable smaTest1 -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smaTest1.dir/link.d CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 43%] Built target smaTest1 -[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 43%] Built target rdForceFieldHelpers -[ 43%] Linking CXX executable testDistGeom -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDistGeom.dir/link.d CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2024.09.6 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/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 -[ 43%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInteractionFields.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 43%] Built target rdAbbreviations -/usr/bin/c++ -fPIC -g -O2 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../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 ../../../lib/libRDKitMolInteractionFields.so.1 ../../../lib/libRDKitMolInteractionFields.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 43%] Built target MolInteractionFields -make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && 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-Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o -MF CMakeFiles/rdMIF.dir/rdMIF.cpp.o.d -o CMakeFiles/rdMIF.dir/rdMIF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap/rdMIF.cpp -[ 44%] Linking CXX shared library ../../../lib/libRDKitDepictor.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolHash/hashfunctions.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -MF CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/normalize.cpp -[ 44%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/DistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 44%] Built target DistGeom -[ 44%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 44%] Built target rdForceField -[ 44%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 44%] Built target DistGeomHelpers -[ 44%] Linking CXX shared library ../../../lib/libRDKitMolHash.so +[ 43%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 -[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2024.09.6 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2024.09.6 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 44%] Built target MolHash +[ 43%] Built target MolHash make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMHFPFingerprint.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -[ 44%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o +[ 43%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 44%] Built target rdMHFPFingerprint -[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdFingerprintGenerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 44%] Built target rdFingerprintGenerator -[ 44%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so +[ 43%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDInchiLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDInchiLib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDInchiLib.so.1 -o ../../lib/libRDKitRDInchiLib.so.1.2024.09.6 CMakeFiles/RDInchiLib.dir/inchi.cpp.o /usr/lib/x86_64-linux-gnu/libinchi.so ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDInchiLib.so.1.2024.09.6 ../../lib/libRDKitRDInchiLib.so.1 ../../lib/libRDKitRDInchiLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 44%] Built target RDInchiLib +[ 43%] Built target RDInchiLib make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 44%] Building CXX object External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o +[ 43%] Building CXX object External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdinchi_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o -MF CMakeFiles/rdinchi.dir/pyInchi.cpp.o.d -o CMakeFiles/rdinchi.dir/pyInchi.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/INCHI-API/Wrap/pyInchi.cpp +[ 43%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInteractionFields.dir/link.txt --verbose=1 +[ 43%] Linking CXX executable testDistGeom +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInteractionFields.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInteractionFields.so.1 -o ../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 ../../../lib/libRDKitMolInteractionFields.so.1 ../../../lib/libRDKitMolInteractionFields.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 43%] Built target MolInteractionFields +make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 44%] Building CXX object Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMIF_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o -MF CMakeFiles/rdMIF.dir/rdMIF.cpp.o.d -o CMakeFiles/rdMIF.dir/rdMIF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap/rdMIF.cpp [ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDistGeom.dir/link.d CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 44%] Built target testDistGeom /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDepictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 44%] Built target rdDepictor -[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMIF.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 44%] Built target rdForceFieldHelpers +[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMHFPFingerprint.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 44%] Built target rdMHFPFingerprint +[ 44%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/DistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 44%] Built target rdMIF +[ 44%] Built target DistGeom [ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdMolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -4393,73 +4408,94 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o [ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CDXMLParser.cpp.o -MF CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o.d -o CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CDXMLParser.cpp +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o [ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -cd 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -MF CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/Mol2FileParser.cpp cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolFileParser.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupParsing.cpp -[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolFileStereochem.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolFileStereochem.cpp +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupParsing.cpp cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MultithreadedMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdinchi.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdinchi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdinchi.so CMakeFiles/rdinchi.dir/pyInchi.cpp.o ../../../lib/libRDKitRDInchiLib.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libinchi.so ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdMIF.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMIF.dir/link.txt --verbose=1 +[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp +[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 48%] Built target rdinchi +[ 48%] Built target rdMIF [ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -4474,665 +4510,711 @@ make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/CoordGen /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/UFF /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/CoordGen 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/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol 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directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testChirality.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/graphmolTest1.dir/test1.cpp.o -MF CMakeFiles/graphmolTest1.dir/test1.cpp.o.d -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/test1.cpp +make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/molopstest.cpp +make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend +[ 50%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o +[ 50%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o +make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -MF CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/resMolSupplierTest.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -MF CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testPicklerGlobalSettings.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol 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cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 49%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/graphmolTest1.dir/test1.cpp.o -MF CMakeFiles/graphmolTest1.dir/test1.cpp.o.d -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/test1.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build make[4]: Entering 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -MF CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o.d -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/testUFFForceField.cpp make -f Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build -[ 49%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/molopstest.cpp -cd 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/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake "--color=" +[ 50%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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-I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/testMolBundle.cpp +[ 51%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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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-I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -MF CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o.d -o CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_graphmol.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol 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-I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/canonTestsCatch.dir/catch_canon.cpp.o -MF CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o.d -o CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_canon.cpp +[ 51%] Building CXX object Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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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../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 51%] Building CXX object Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/FileParsers/testAtropisomers.cpp +[ 52%] Linking CXX executable graphmolSGroupCatch +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/FileParsers/testSquiggleDoubleBonds.cpp +[ 52%] Linking CXX executable canonTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ChemReactions/MDLParser.cpp +[ 52%] Linking CXX executable molopsTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build -make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build +[ 52%] Built target molopsTestsCatch +make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -MF CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o.d -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testGeneralFileReader.cpp +[ 52%] Linking CXX executable testSGroup +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -MF CMakeFiles/depictorCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/catch_tests.cpp -[ 51%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 51%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/testDepictor.cpp +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp +[ 52%] Linking CXX executable testAtropisomers +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAtropisomers.dir/link.txt --verbose=1 +[ 52%] Linking CXX executable nontetrahedralCatch +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAtropisomers.dir/link.d CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -o testAtropisomers ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 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target testAtropisomers +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/FileParsers/file_parsers_catch.cpp -[ 52%] Linking CXX executable testSequence -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 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../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 54%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 52%] Built target testExtendedStereoParsing +[ 54%] Built target testSequence 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-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 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-o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionRunner.cpp -[ 53%] Linking CXX executable graphmolOrganometallicsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolOrganometallicsCatch.dir/link.txt --verbose=1 -[ 53%] Linking CXX executable testAtropisomers -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAtropisomers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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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CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolOrganometallicsCatch.dir/link.d CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -o graphmolOrganometallicsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 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-DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/FileParsers/connectTheDots_catch.cpp -[ 53%] Linking CXX executable testMultithreadedMolSupplier -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 -[ 53%] Linking CXX executable molopsTestsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molopsTestsCatch.dir/link.txt --verbose=1 -[ 53%] Linking CXX executable nontetrahedralCatch -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +[ 55%] Linking CXX executable testExtendedStereoParsing +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 53%] Built target testMultithreadedMolSupplier -[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 55%] Built target testExtendedStereoParsing +[ 55%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp +[ 55%] Linking CXX executable graphmoltestChirality +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestChirality.dir/link.d CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ChemReactions/PreprocessRxn.cpp +[ 55%] Built target graphmoltestChirality make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/depend -[ 53%] Built target molopsTestsCatch +[ 56%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ChemReactions/ReactionUtils.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build -[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/SanitizeRxn.cpp -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o +[ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -MF CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o.d -o CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/v2_suppliers_catch.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 53%] Built target nontetrahedralCatch -[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/PNGParser.cpp -[ 53%] Linking CXX executable resMolSupplierTest -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 -[ 54%] Linking CXX executable testGeneralFileReader -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGeneralFileReader.dir/link.d CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -fpermissive -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp -[ 54%] Linking CXX executable graphmoltestPicklerGlobalSetting -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 +[ 56%] Built target connectTheDotsTest make -f 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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-202409.6/Code/GraphMol/ChemReactions/PreprocessRxn.cpp +[ 56%] Linking CXX executable XYZFileParserCatchTest +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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 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/usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickleTestsCatch.dir/link.txt --verbose=1 -[ 54%] Built target graphmoltestPicklerGlobalSetting -[ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp +[ 56%] Built target XYZFileParserCatchTest +[ 56%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/SanitizeRxn.cpp +[ 56%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/PNGParser.cpp +[ 56%] Linking CXX executable v2MolSuppliers +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2MolSuppliers.dir/link.txt --verbose=1 +[ 56%] Linking CXX executable testMolWriter +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2MolSuppliers.dir/link.d CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -o v2MolSuppliers ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -MF CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o.d -o CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/multithreaded_supplier_catch.cpp -[ 54%] Linking CXX executable testUFFForceField -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pickleTestsCatch.dir/link.d CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -o pickleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 54%] Built target pickleTestsCatch +[ 56%] Built target v2MolSuppliers make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake "--color=" +[ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -MF CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o.d -o CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/multithreaded_supplier_catch.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 54%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o +[ 56%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 56%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code 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-I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms/catch_tests.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem 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../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 57%] Built target smiTest1 make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering 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../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 57%] Built target testSGroup +[ 57%] Built target filterCatalogTest 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-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 57%] Built target molfileStereoCatchTest [ 57%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/Fingerprints/catch_tests.cpp -[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && 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../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 57%] Linking CXX executable chiralityTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script 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../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 60%] Built target testMMFFForceField +[ 60%] Built target testChemTransforms make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MORSE.cpp.o -MF CMakeFiles/Descriptors.dir/MORSE.cpp.o.d -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MORSE.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp -[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/WHIM.cpp +[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Data3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp +[ 60%] Linking CXX executable testMolTransforms +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolTransforms.dir/link.d CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 60%] Built target testMolTransforms make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 62%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o +[ 61%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/DistGeomHelpers/catch_tests.cpp -[ 62%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong 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../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp +[ 61%] Linking CXX executable molTransformsTestCatch +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTransformsTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 62%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o +[ 61%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp -[ 62%] Linking CXX executable depictorCatch -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 61%] Built target rdfragcatalog make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 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"--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 62%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o +[ 61%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/test1.cpp -[ 62%] Linking CXX executable substructTestCatch -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 -[ 62%] Linking CXX executable testMolTransforms -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build +make[4]: Entering directory 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so +[ 62%] Linking CXX executable testMMFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -[ 63%] Built target ChemReactions +[ 62%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalMCES.cpp -[ 64%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SubstructMatchCustom.cpp -[ 64%] Linking CXX executable testMMFFForceFieldHelpersMultiThread -cd 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalCluster.cpp -[ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -c 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 65%] Built target testMMFFForceFieldHelpersMultiThread -[ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 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-[ 65%] Linking CXX executable forceFieldHelpersCatch -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/forceFieldHelpersCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/forceFieldHelpersCatch.dir/link.d CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -o forceFieldHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitOptimizer.so.1.2024.09.6 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalResult.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalResult.cpp -[ 65%] Linking CXX executable fpGenTestCatch -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.cpp -[ 66%] Linking CXX executable testCrystalForceField -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFingerprintGenerators.dir/link.d CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 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-I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Deprotect/Deprotect.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -MF CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o.d -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/LinkNode.cpp -[ 66%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/RepeatUnit.cpp -[ 66%] Linking CXX executable testShapeHelpers -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script 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Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSet.cpp -[ 66%] Linking CXX executable testMolCatalog -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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 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/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.cpp -[ 66%] Linking CXX executable molAlignCatchTest -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 64%] Linking CXX executable testFeatures +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 66%] Built target molAlignCatchTest +[ 64%] Built target testFeatures make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 66%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o +[ 64%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -MF CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o.d -o CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/molinterchange_catch.cpp -[ 66%] Linking CXX executable testMMFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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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-DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp +[ 64%] Linking CXX executable testFingerprints +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFingerprints.dir/link.d CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 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Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.cpp -[ 66%] Linking CXX executable testChemTransforms -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 +[ 64%] Built target testFingerprints make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make 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Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o +[ 64%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 66%] Built target testChemTransforms -[ 66%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MolOps.cpp -[ 66%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -MF CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o.d -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/ChiralityOps.cpp -[ 66%] Linking CXX shared library ../../../lib/libRDKitMMPA.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2024.09.6 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so +[ 64%] Linking CXX executable testUFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -MF CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o.d -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/catch_tests.cpp +[ 64%] Linking CXX shared library ../../../lib/libRDKitMMPA.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/build.make Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/build +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2024.09.6 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 64%] Built target Deprotect +[ 65%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinParser.cpp -[ 66%] Linking CXX executable smiTest1 -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 +[ 66%] Built target molHashCatchTest make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp +[ 67%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -MF CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o.d -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp -[ 67%] Built target graphmolTestsCatch +[ 67%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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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-202409.6/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp +[ 67%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SubstructMatchCustom.cpp +[ 67%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolProcessing.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolProcessing.so.1.2024.09.6 ../../../lib/libRDKitMolProcessing.so.1 ../../../lib/libRDKitMolProcessing.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 67%] Built target MolProcessing make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake "--color=" @@ -5682,9 +5768,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 67%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o cd 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 67%] Linking CXX executable testDistGeomHelpers +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.6 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 67%] Built target testUFFForceFieldHelpers +[ 67%] Built target testDistGeomHelpers make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake "--color=" @@ -5693,25 +5781,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 67%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Pipeline.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Pipeline.cpp.o -MF CMakeFiles/MolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/MolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Pipeline.cpp -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-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -cd 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../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 67%] Built target trajectoryTest -[ 67%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so -[ 67%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/Deprotect.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolStandardize.cpp.o -MF CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o.d -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 67%] Built target Deprotect +[ 67%] Built target molInterchangeCatchTest 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-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake "--color=" @@ -5720,34 +5794,32 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 67%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp +[ 68%] Linking CXX executable testReactionFingerprints +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o +[ 68%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp -[ 67%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp -[ 67%] Linking CXX executable testFingerprintGenerators -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 -[ 67%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Metal.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFingerprintGenerators.dir/link.d CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 67%] Built target testFingerprintGenerators -[ 67%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/MolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Normalize.cpp -[ 67%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp -[ 68%] Linking CXX executable molHashCatchTest -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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-I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/DrawMol.cpp +[ 68%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -MF CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o.d -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/MolStandardize.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAbbreviations.dir/link.d CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -o testAbbreviations ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitAbbreviations.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 68%] Built target molHashCatchTest -[ 68%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolStandardize/Validate.cpp +[ 68%] Built target testAbbreviations make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake "--color=" @@ -5756,234 +5828,234 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -MF CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o.d -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/deprotectTest.cpp -[ 69%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Charge.cpp -[ 69%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolProcessing.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolProcessing.so.1.2024.09.6 ../../../lib/libRDKitMolProcessing.so.1 ../../../lib/libRDKitMolProcessing.so +[ 68%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK 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../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 69%] Built target MolProcessing +[ 68%] Built target testMIF make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make 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CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 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/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MORSE.cpp.o -MF CMakeFiles/Descriptors.dir/MORSE.cpp.o.d -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MORSE.cpp +[ 68%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp -[ 69%] Linking CXX shared library ../../../lib/libRDKitFMCS.so +[ 68%] Built target testMMPA +[ 68%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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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-202409.6/Code/GraphMol/MolStandardize/Metal.cpp +[ 68%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -MF CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o.d -o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/PartitionSet.cpp +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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CMakeFiles/Descriptors.dir/GETAWAY.cpp.o.d -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/GETAWAY.cpp +[ 68%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 +[ 68%] Linking CXX executable testEnumeration +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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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CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Tautomer.cpp -[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp -[ 70%] Linking CXX executable testFingerprints -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 -[ 70%] Linking CXX shared module 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../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp -[ 70%] Linking CXX executable chiralityTestsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 70%] Built target molInterchangeTest1 -[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 70%] Built target chiralityTestsCatch -[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ 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../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 70%] Built target testDistGeomHelpers -[ 70%] Linking CXX executable fileParsersCatchTest -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 -[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/AcidBaseCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o.d -o 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../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 70%] Built target fileParsersCatchTest -[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -cd 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp -[ 70%] Linking CXX executable molInterchangeCatchTest -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 -[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp -[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp -[ 71%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/RascalMCES.dir/link.txt --verbose=1 +[ 69%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp -[ 71%] Linking CXX executable testMIF -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMIF.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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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../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 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.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -[ 71%] Built target testMIF -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 ../../../lib/libRDKitRascalMCES.so.1 ../../../lib/libRDKitRascalMCES.so -[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Charge.cpp +[ 70%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 +[ 70%] Linking CXX shared module ../../../../rdkit/Chem/rdMolProcessing.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolProcessing.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolProcessing.so CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o ../../../../lib/libRDKitMolProcessing.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDStreams.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 70%] Built target rdMolProcessing +[ 70%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 70%] Built target MolEnumerator +make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 70%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/enumerator_catch.cpp +[ 70%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.cpp +In file included from /usr/include/c++/14/vector:62, + from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: +In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', + inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, + inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, + inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, + inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1022:38, + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, + inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.6/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/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/vector:63: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', + inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, + inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, + inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1013:40, + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, + inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.6/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))); + | ^ +[ 70%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinDefs.cpp +[ 70%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/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 -DrdMolEnumerator_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem 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-I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawShape.cpp +[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o +cd 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 70%] Built target FMCStest +[ 70%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp +[ 70%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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.1.2024.09.6 CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 ../../../lib/libRDKitRascalMCES.so.1 ../../../lib/libRDKitRascalMCES.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 70%] Built target RascalMCES make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp +[ 71%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 73%] Built target rdmolops +[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp +[ 73%] Linking CXX executable rxnTestCatch +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong 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/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 ../../../lib/libRDKitSynthonSpaceSearch.so.1 ../../../lib/libRDKitSynthonSpaceSearch.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 73%] Built target SynthonSpaceSearch make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu 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CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/Wrap/rdSynthonSpaceSearch.cpp -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake "--color=" +[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp +[ 74%] Linking CXX executable testRascalCluster +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 +[ 74%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalCluster.dir/link.d CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 73%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/enumerator_catch.cpp -[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp -[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFT.cpp -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' 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CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp +[ 74%] Linking CXX executable testFMCS +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 +[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o.d -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp -[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp +[ 75%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so +cd 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../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd 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CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend +[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp +[ 75%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp +[ 75%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp +make -f 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testBCUT.dir/testBCUT.cpp.o -MF CMakeFiles/testBCUT.dir/testBCUT.cpp.o.d -o CMakeFiles/testBCUT.dir/testBCUT.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testBCUT.cpp +make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testRDFcustom.dir/testRDFcustom.cpp.o -MF CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o.d -o CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -c 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build +[ 77%] Built target rdRascalMCES +make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu 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-DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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-I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/testPBF.cpp.o -MF CMakeFiles/testPBF.dir/testPBF.cpp.o.d -o CMakeFiles/testPBF.dir/testPBF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testPBF.cpp -[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -[ 74%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -[ 74%] Building CXX object 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testBCUT.dir/testBCUT.cpp.o -MF CMakeFiles/testBCUT.dir/testBCUT.cpp.o.d -o CMakeFiles/testBCUT.dir/testBCUT.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testBCUT.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /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-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testDescriptors.dir/test.cpp.o -MF CMakeFiles/testDescriptors.dir/test.cpp.o.d -o CMakeFiles/testDescriptors.dir/test.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/test.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o -MF CMakeFiles/testATF.dir/testATF.cpp.o.d -o CMakeFiles/testATF.dir/testATF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testATF.cpp +[ 78%] Linking CXX executable testMolEnumerator +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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 CMakeFiles/testWHIM.dir/testWHIM.cpp.o.d -o CMakeFiles/testWHIM.dir/testWHIM.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testWHIM.cpp -In file included from /usr/include/c++/14/vector:62, - from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: -In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', - inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, - inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, - inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, - inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1022:38, - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, - inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.6/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/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/vector:63: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', - inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, - inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, - inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1013:40, - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, - inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.6/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))); - | ^ -[ 77%] Linking CXX executable fileParsersTest1 -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdDeprotect.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDeprotect.so CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o ../../../../lib/libRDKitDeprotect.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testGETAWAY.dir/testGETAWAY.cpp.o -MF CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o.d -o CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testGETAWAY.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolEnumerator.dir/link.d CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 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directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 77%] Built target fileParsersTest1 +[ 80%] Built target testMolEnumerator make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -MF CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o.d -o CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testAUTOCORR3D.cpp make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' @@ -6186,593 +6277,457 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o +[ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/testCoulombMat.dir/testCoulombMat.cpp.o -MF CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o.d -o CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testCoulombMat.cpp +[ 80%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/MolStandardize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 CMakeFiles/MolStandardize.dir/Pipeline.cpp.o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o CMakeFiles/MolStandardize.dir/Metal.cpp.o CMakeFiles/MolStandardize.dir/Normalize.cpp.o CMakeFiles/MolStandardize.dir/Validate.cpp.o CMakeFiles/MolStandardize.dir/Charge.cpp.o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o CMakeFiles/MolStandardize.dir/Fragment.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 80%] Built target MolStandardize make -f Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 77%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o +[ 80%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp -[ 77%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so -cd 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CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 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../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 77%] Built target MolStandardize -make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend +[ 80%] Built target testBCUT make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend -make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend -make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend -make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend -make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 80%] Built target testRascalMCES +make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake "--color=" +[ 80%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -MF CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o.d -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/testNormalize.cpp +[ 80%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MarvinParser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 80%] Built target MarvinParser +make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 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/usr/lib/x86_64-linux-gnu/libcairo.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 80%] Built target MolDraw2D +make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 80%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 -[ 80%] Built target testWHIM -[ 80%] Linking CXX executable testRDFcustom -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDFcustom.dir/link.txt --verbose=1 -[ 80%] Linking CXX executable test3D -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/test3D.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong 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Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/depend -make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend -make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend -make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu 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../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 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-ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp -[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 -[ 83%] Linking CXX executable graphmolMolOpsTest -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. 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../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 +[ 84%] Built target molStandardizeSmallTest +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend 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-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 -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +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-202409.6/obj-x86_64-linux-gnu' +[ 84%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -MF CMakeFiles/moldraw2DTest1.dir/test1.cpp.o.d -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/test1.cpp +[ 84%] Linking CXX executable molChargeTest +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 +[ 85%] Linking CXX executable molValidateTest +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molChargeTest.dir/link.d CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 83%] Built target graphmolMolOpsTest -[ 83%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MaeMolSupplier.cpp -[ 83%] Linking CXX executable molStandardizeSmallTest -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeSmallTest.dir/link.d CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 85%] Built target molChargeTest +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/Atom.cpp -[ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/catch_tests.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molValidateTest.dir/link.d CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/obj-x86_64-linux-gnu' +[ 86%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS 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testRascalMCES -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalMCES.dir/link.txt --verbose=1 -[ 88%] Linking CXX executable molValidateTest -[ 88%] Linking CXX executable testFMCS -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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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CMakeFiles/rdchem.dir/rdchem.cpp.o.d -o CMakeFiles/rdchem.dir/rdchem.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rdchem.cpp +[ 86%] Linking CXX executable molStandardizeTest +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeTest.dir/link.d CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 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Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -MF CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o.d -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rdmolfiles.cpp +[ 86%] Linking CXX executable testDescriptors +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDescriptors.dir/link.d CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2024.09.6 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-I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SmilesMolSupplier.cpp -[ 88%] Linking CXX executable molFragmentTest -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/testO3AAlign.cpp -[ 88%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so +[ 86%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 +[ 86%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.6 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeTest.dir/link.d CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 88%] Built target ScaffoldNetwork +[ 86%] Built target ScaffoldNetwork 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-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap 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Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -MF CMakeFiles/rdchem.dir/EditableMol.cpp.o.d -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/EditableMol.cpp -[ 89%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 -[ 89%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +[ 86%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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/usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 89%] Built target rdmolops -[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Mancude.cpp -[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings 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../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 89%] Built target testGenericGroups -[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp -[ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp -[ 90%] Linking CXX executable testMrvToMol -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/obj-x86_64-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -cd 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/build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.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, @@ -6820,185 +6775,301 @@ /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 94%] Linking CXX executable testO3AAlign -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 -make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend +[ 87%] Linking CXX executable molStandardizeCatchTest +cd 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'/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 90%] Built target rdTautomerQuery +[ 91%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code 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+cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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&& /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Pipeline.cpp +[ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Sort.cpp +[ 92%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ 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-DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MaeWriter.cpp +[ 93%] Building CXX object 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-I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolBundle.cpp.o -MF CMakeFiles/rdchem.dir/MolBundle.cpp.o.d -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MolBundle.cpp [ 94%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 95%] Built target rdMolStandardize -[ 95%] Linking CXX executable moldraw2DRxnTest1 -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong 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CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -o testCIPLabeler ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 96%] Built target testCIPLabeler -[ 96%] Linking CXX executable testScaffoldNetwork -cd 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-MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp +[ 95%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp +make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build +[ 95%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -MF CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/catch_tests.cpp +[ 95%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/PatternFactory.cpp +make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build +make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 96%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o +[ 95%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeneralizedSubstruct_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -MF CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o.d -o CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/Wrap/rdGeneralizedSubstruct.cpp +make -f Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/build.make Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -MF CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/catch_tests.cpp -[ 96%] Building CXX object 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/PatternFactory.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o -[ 96%] Building CXX object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/adapter.cpp.o -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o -MF CMakeFiles/rdkit.dir/cache.c.o.d -o CMakeFiles/rdkit.dir/cache.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/cache.c -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o +[ 95%] Building CXX object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/adapter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/adapter.cpp.o -MF CMakeFiles/rdkit.dir/adapter.cpp.o.d -o CMakeFiles/rdkit.dir/adapter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o -MF CMakeFiles/rdkit.dir/low_gist.c.o.d -o CMakeFiles/rdkit.dir/low_gist.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/low_gist.c +[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-202409.6/Code/PgSQL/rdkit/bfp_op.c -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o -[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o -[ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bitstring.c.o +[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o -MF CMakeFiles/rdkit.dir/cache.c.o.d -o CMakeFiles/rdkit.dir/cache.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/cache.c +[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-202409.6/Code/PgSQL/rdkit/guc.c +[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o -MF CMakeFiles/rdkit.dir/low_gist.c.o.d -o CMakeFiles/rdkit.dir/low_gist.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/low_gist.c +[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o -MF CMakeFiles/rdkit.dir/mol_op.c.o.d -o CMakeFiles/rdkit.dir/mol_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/mol_op.c +[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o -MF CMakeFiles/rdkit.dir/rdkit_gist.c.o.d -o CMakeFiles/rdkit.dir/rdkit_gist.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/rdkit_gist.c +[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-202409.6/Code/PgSQL/rdkit/bfp_gist.c -[ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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 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cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 +[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gin.c.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql 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Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o +[ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o -MF CMakeFiles/rdkit.dir/sfp_op.c.o.d -o CMakeFiles/rdkit.dir/sfp_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/sfp_op.c -[ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_io.c.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/rdkit_io.c -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdTautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp +/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp: In function 'void* makeAvalonBFP(CROMol, bool, unsigned int)': +/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1627:38: warning: unused parameter 'data' [-Wunused-parameter] + 1627 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, + | ~~~~~~~^~~~ +/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1627:49: warning: unused parameter 'isQuery' [-Wunused-parameter] + 1627 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, + | ~~~~~^~~~~~~ +/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1628:44: warning: unused parameter 'bitFlags' [-Wunused-parameter] + 1628 | unsigned int bitFlags) { + | ~~~~~~~~~~~~~^~~~~~~~ +[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdChemReactions.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o 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../../../lib/libRDKitRGroupDecomposition.so [ 97%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o 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-I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -MF CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o.d -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp [ 97%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -cd 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-I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -MF CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o.d -o CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp +[ 97%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/GaExample.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -MF CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o.d -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdmolfiles.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 97%] Built target rdmolfiles -/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp: In function 'void* makeAvalonBFP(CROMol, bool, unsigned int)': -/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1627:38: warning: unused parameter 'data' [-Wunused-parameter] - 1627 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, - | ~~~~~~~^~~~ -/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1627:49: warning: unused parameter 'isQuery' [-Wunused-parameter] - 1627 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, - | ~~~~~^~~~~~~ -/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1628:44: warning: unused parameter 'bitFlags' [-Wunused-parameter] - 1628 | unsigned int bitFlags) { - | ~~~~~~~~~~~~~^~~~~~~~ +[ 97%] Linking CXX executable generalizedSubstructCatch +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdchem.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 97%] Built target rdchem -[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/rdChemReactions.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitMarvinParser.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 97%] Built target rdChemReactions -[ 97%] Linking CXX executable moldraw2DTest1 -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTest1.dir/link.d CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 97%] Built target moldraw2DTest1 [ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeneralizedSubstruct.dir/link.txt --verbose=1 -[ 97%] Linking CXX executable testRGroupDecompInternals -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdGeneralizedSubstruct.so CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so 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../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 97%] Built target rdGeneralizedSubstruct -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecompInternals.dir/link.d CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 97%] Built target testRGroupDecompInternals -[ 97%] Linking CXX executable gaExample -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 97%] Built target gaExample -[ 97%] Linking CXX executable generalizedSubstructCatch -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/generalizedSubstructCatch.dir/link.d CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -o generalizedSubstructCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 97%] Built target generalizedSubstructCatch [ 97%] Linking CXX shared library librdkit.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-202409.6/Code/PgSQL/rdkit/lib /usr/lib/x86_64-linux-gnu/libpq.so ../../../lib/libRDKitRDInchiLib.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libinchi.so ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitMolHash.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 @@ -7089,39 +7130,26 @@ cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/expected make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 97%] Built target rdkit -[ 97%] Linking CXX executable rgroupCatchTests -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rgroupCatchTests.dir/link.d CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 97%] Built target rgroupCatchTests -[ 97%] Linking CXX executable testReaction -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReaction.dir/link.d CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 97%] Built target testReaction -[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdRGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../../lib/libRDKitga.so.1.2024.09.6 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 97%] Built target rdRGroupDecomposition [ 97%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 +[ 97%] Linking CXX executable gaExample +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 97%] Built target SubstructLibrary make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/depend make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' @@ -7129,53 +7157,61 @@ make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/catch_tests.cpp [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/x86_64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolDraw2D.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 99%] Built target rdMolDraw2D -[ 99%] Linking CXX executable testRGroupDecomp -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 99%] Built target gaExample +[ 99%] Linking CXX executable testRGroupDecompInternals +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecompInternals.dir/link.d CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 99%] Built target testRGroupDecomp +[ 99%] Built target testRGroupDecompInternals +[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 +[ 99%] Linking CXX executable rgroupCatchTests +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdRGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../../lib/libRDKitga.so.1.2024.09.6 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 99%] Built target rdRGroupDecomposition +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rgroupCatchTests.dir/link.d CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 99%] Built target rgroupCatchTests [ 99%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 +[ 99%] Linking CXX executable testSynthonSpaceSubstructureSearch +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_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.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +/usr/bin/ld: make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 99%] Built target substructLibraryCatchTest +CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o: in function `CATCH2_INTERNAL_TEST_20()': +./obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/./Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp:306:(.text+0x7a8f): warning: the use of `tmpnam' is dangerous, better use `mkstemp' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.d CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -o testSynthonSpaceSubstructureSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +[ 99%] Built target testSynthonSpaceSubstructureSearch [ 99%] Linking CXX executable substructLibraryTest cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryTest.dir/link.d CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' [ 99%] Built target substructLibraryTest -[ 99%] Linking CXX executable testSynthonSpaceSubstructureSearch -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.txt --verbose=1 -/usr/bin/ld: CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o: in function `CATCH2_INTERNAL_TEST_20()': -./obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/./Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp:306:(.text+0x7a8f): warning: the use of `tmpnam' is dangerous, better use `mkstemp' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.d CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -o testSynthonSpaceSubstructureSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 99%] Built target testSynthonSpaceSubstructureSearch -[ 99%] Linking CXX executable moldraw2DTestCatch -cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTestCatch.dir/link.d CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitCIPLabeler.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 99%] Linking CXX executable testRGroupDecomp +cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -[ 99%] Built target moldraw2DTestCatch +[ 99%] Built target testRGroupDecomp [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -7307,77 +7343,77 @@ Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GenericGroups Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Test +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Trajectory +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Fonts -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt/Demo -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/libs -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/tutorial +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/data -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Trajectory -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/data -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/tutorial -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GenericGroups -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DetermineBonds -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Test -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Qt/Demo +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Fonts +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/StructChecker -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/data +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/GraphMol/libs Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Catalogs Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/DataStructs Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Query Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ML -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ML/Data -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ML/Cluster Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ML/Cluster/Murtagh +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/DataManip Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers @@ -7387,12 +7423,12 @@ Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/RDBoost Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/DistGeom Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ForceField -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Numerics -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment -Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Numerics/EigenSolvers +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer +Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Geometry Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/Features Searching for files in directory /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures @@ -8408,6 +8444,11 @@ Generating code for file Contrib.h... Generating code for file DistanceConstraints.h... Generating code for file ForceField.h... +Generating code for file OopBend.h... +Generating code for file StretchBend.h... +Generating code for file TorsionConstraint.h... +Generating code for file TorsionConstraint.h... +Generating code for file TorsionConstraint.h... Generating code for file AngleBend.h... Generating code for file AngleBend.h... Generating code for file AngleConstraint.h... @@ -8420,22 +8461,17 @@ Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... +Generating code for file Inversion.h... +Generating code for file Inversions.h... Generating code for file Nonbonded.h... Generating code for file Nonbonded.h... -Generating code for file OopBend.h... Generating code for file Params.h... Generating code for file Params.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... -Generating code for file StretchBend.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngle.h... -Generating code for file TorsionConstraint.h... -Generating code for file TorsionConstraint.h... -Generating code for file TorsionConstraint.h... -Generating code for file Inversion.h... -Generating code for file Inversions.h... Generating code for file Utils.h... Generating code for file Utils.h... Generating code for file Grid3D.h... @@ -8534,8 +8570,6 @@ Generating code for file RegisterDescriptor.h... Generating code for file USRDescriptor.h... Generating code for file WHIM.h... -Generating code for file details.h... -Generating code for file details.h... Generating code for file DetermineBonds.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Embedder.h... @@ -8592,11 +8626,11 @@ Generating code for file TorsionAngleM6.h... Generating code for file TorsionPreferences.h... Generating code for file FFConvenience.h... +Generating code for file MMFF.h... Generating code for file AtomTyper.h... Generating code for file AtomTyper.h... Generating code for file Builder.h... Generating code for file Builder.h... -Generating code for file MMFF.h... Generating code for file UFF.h... Generating code for file FragCatalogEntry.h... Generating code for file FragCatalogUtils.h... @@ -8655,6 +8689,8 @@ Generating code for file MolHash.h... Generating code for file nmmolhash.h... Generating code for file MIFDescriptors.h... +Generating code for file details.h... +Generating code for file details.h... Generating code for file MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.h... @@ -8853,6 +8889,11 @@ Generating docs for file Contrib.h... Generating docs for file DistanceConstraints.h... Generating docs for file ForceField.h... +Generating docs for file OopBend.h... +Generating docs for file StretchBend.h... +Generating docs for file TorsionConstraint.h... +Generating docs for file TorsionConstraint.h... +Generating docs for file TorsionConstraint.h... Generating docs for file AngleBend.h... Generating docs for file AngleBend.h... Generating docs for file AngleConstraint.h... @@ -8865,22 +8906,17 @@ Generating docs for file DistanceConstraint.h... Generating docs for file DistanceConstraint.h... Generating docs for file DistanceConstraint.h... +Generating docs for file Inversion.h... +Generating docs for file Inversions.h... Generating docs for file Nonbonded.h... Generating docs for file Nonbonded.h... -Generating docs for file OopBend.h... Generating docs for file Params.h... Generating docs for file Params.h... Generating docs for file PositionConstraint.h... Generating docs for file PositionConstraint.h... Generating docs for file PositionConstraint.h... -Generating docs for file StretchBend.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionAngle.h... -Generating docs for file TorsionConstraint.h... -Generating docs for file TorsionConstraint.h... -Generating docs for file TorsionConstraint.h... -Generating docs for file Inversion.h... -Generating docs for file Inversions.h... Generating docs for file Utils.h... Generating docs for file Utils.h... Generating docs for file Grid3D.h... @@ -8979,8 +9015,6 @@ Generating docs for file RegisterDescriptor.h... Generating docs for file USRDescriptor.h... Generating docs for file WHIM.h... -Generating docs for file details.h... -Generating docs for file details.h... Generating docs for file DetermineBonds.h... Generating docs for file BoundsMatrixBuilder.h... Generating docs for file Embedder.h... @@ -9037,11 +9071,11 @@ Generating docs for file TorsionAngleM6.h... Generating docs for file TorsionPreferences.h... Generating docs for file FFConvenience.h... +Generating docs for file MMFF.h... Generating docs for file AtomTyper.h... Generating docs for file AtomTyper.h... Generating docs for file Builder.h... Generating docs for file Builder.h... -Generating docs for file MMFF.h... Generating docs for file UFF.h... Generating docs for file FragCatalogEntry.h... Generating docs for file FragCatalogUtils.h... @@ -9100,6 +9134,8 @@ Generating docs for file MolHash.h... Generating docs for file nmmolhash.h... Generating docs for file MIFDescriptors.h... +Generating docs for file details.h... +Generating docs for file details.h... Generating docs for file MolInterchange.h... Generating docs for file MolOps.h... Generating docs for file MolPickler.h... @@ -11251,9 +11287,9 @@ copying downloadable files... [100%] C++Examples/example16.cpp copying static files... -Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/html/_static/basic.css +Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/html/_static/sphinxdoc.css copying static files: done copying extra files... @@ -12539,10 +12575,10 @@ done preparing documents... done copying assets... -copying TeX support files... Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/Makefile -Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/latexmkjarc +copying TeX support files... Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/make.bat +Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/Makefile Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/latexmkrc -Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/make.bat +Writing evaluated template result to /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/latexmkjarc done copying assets: done processing RDKit.tex... @@ -12810,7 +12846,7 @@ resolving references... /build/reproducible-path/rdkit-202409.6/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 @@ -14938,10 +14974,10 @@ find /build/reproducible-path/rdkit-202409.6 -name rdchem.so /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so PYTHONPATH=/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/:/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib:" dh_auto_test - cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 + cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 make[2]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j42 +/usr/bin/ctest --force-new-ctest-process --verbose -j20 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. @@ -15075,138 +15111,6 @@ 20: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/geometryTestsCatch 20: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/Code/Geometry/Wrap/testGeometry.py" -21: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/Wrap -21: Test timeout computed to be: 1500 -test 22 - Start 22: testMatrices - -22: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/testMatrices -22: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics -22: Test timeout computed to be: 1500 -test 23 - Start 23: testConrec - -23: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/testConrec -23: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics -23: Test timeout computed to be: 1500 -test 24 - Start 24: testAlignment - -24: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment/testAlignment -24: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment -24: Test timeout computed to be: 1500 -test 25 - Start 25: pyAlignment - -25: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/Wrap/testAlignment.py" -25: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap -25: Test timeout computed to be: 1500 -test 26 - Start 26: testOptimizer - -26: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/testOptimizer -26: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer -26: Test timeout computed to be: 1500 -test 27 - Start 27: ForceFieldsCatch - -27: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/ForceFieldsCatch -27: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField -27: Test timeout computed to be: 1500 -test 28 - Start 28: testUFFForceField - -28: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/UFF/testUFFForceField -28: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/UFF -28: Test timeout computed to be: 1500 -test 29 - Start 29: testMMFFForceField - -29: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField -29: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/MMFF -29: Test timeout computed to be: 1500 -test 30 - Start 30: pyForceFieldConstraints - -30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ForceField/Wrap/testConstraints.py" -30: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/Wrap -30: Test timeout computed to be: 1500 -test 31 - Start 31: testDistGeom - -31: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom/testDistGeom -31: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom -31: Test timeout computed to be: 1500 -test 32 - Start 32: pyDistGeom - -32: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DistGeom/Wrap/rough_test.py" -32: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom/Wrap -32: Test timeout computed to be: 1500 -test 33 - Start 33: graphmolTest1 - -33: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -33: Test timeout computed to be: 1500 -test 34 - Start 34: graphmolcpTest - -34: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolcpTest -34: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -34: Test timeout computed to be: 1500 -test 35 - Start 35: graphmolqueryTest - -35: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest -35: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -35: Test timeout computed to be: 1500 -test 36 - Start 36: graphmolMolOpsTest - -36: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMolOpsTest -36: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -36: Test timeout computed to be: 1500 -test 37 - Start 37: graphmoltestChirality - -37: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestChirality -37: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -37: Test timeout computed to be: 1500 -test 38 - Start 38: graphmoltestPickler - -38: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPickler -38: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -38: Test timeout computed to be: 1500 -test 39 - Start 39: graphmoltestPicklerGlobalSetting - -39: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting -39: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -39: Test timeout computed to be: 1500 -test 40 - Start 40: graphmolIterTest - -40: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolIterTest -40: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -40: Test timeout computed to be: 1500 -test 41 - Start 41: hanoiTest - -41: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest -41: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -41: Test timeout computed to be: 1500 -test 42 - Start 42: graphmolMemTest1 - -42: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 -42: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -42: Test timeout computed to be: 1500 1: core 1: RDKit 2D 1: @@ -15664,41 +15568,41 @@ 1: 2 5 1 0 1: M END 1: -3: [12:00:54] Testing Github940: property dictionaries leaking memory -3: [12:00:54] done +3: [09:20:23] Testing Github940: property dictionaries leaking memory +3: [09:20:23] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect -3: static boost any:0.000392 s -3: dynamic boost any:0.001755 s -3: static RDAny:0.000224 s -3: dynamic RDAny:0.001623 s -3: static RDValue:2e-06 s -3: dynamic RDValue:0.000276 s +3: static boost any:0.000515 s +3: dynamic boost any:0.001847 s +3: static RDAny:0.000343 s +3: dynamic RDAny:0.00181 s +3: static RDValue:1e-06 s +3: dynamic RDValue:0.000278 s 3: deleted! -3: [12:00:54] ------------------------------------- -3: [12:00:54] Testing String Pickle Roundtrips. -3: [12:00:54] done -3: [12:00:54] ------------------------------------- -3: [12:00:54] Testing conversion of vect to string. -3: [12:00:54] done -3: [12:00:54] ------------------------------------- -3: [12:00:54] Testing returning const references. -3: [12:00:54] any cast -3: [12:00:54] done: 0.001058 300000 -3: [12:00:54] copy -3: [12:00:54] done: 0.001107 300000 -3: [12:00:54] ref -3: [12:00:54] done: 0.001114 300000 -3: [12:00:54] dict -3: [12:00:54] done: 0.002845 300000 -3: [12:00:54] ref with hasVal -3: [12:00:54] done: 0.001825 300000 -3: [12:00:54] done -3: [12:00:54] ------------------------------------- -3: [12:00:54] Testing dict update. -3: [12:00:54] done +3: [09:20:23] ------------------------------------- +3: [09:20:23] Testing String Pickle Roundtrips. +3: [09:20:23] done +3: [09:20:23] ------------------------------------- +3: [09:20:23] Testing conversion of vect to string. +3: [09:20:23] done +3: [09:20:23] ------------------------------------- +3: [09:20:23] Testing returning const references. +3: [09:20:23] any cast +3: [09:20:23] done: 0.001273 300000 +3: [09:20:23] copy +3: [09:20:23] done: 0.001252 300000 +3: [09:20:23] ref +3: [09:20:23] done: 0.001439 300000 +3: [09:20:23] dict +3: [09:20:23] done: 0.003561 300000 +3: [09:20:23] ref with hasVal +3: [09:20:23] done: 0.00195 300000 +3: [09:20:23] done +3: [09:20:23] ------------------------------------- +3: [09:20:23] Testing dict update. +3: [09:20:23] done 3: deleted! 3: deleted! 3: deleted! @@ -15717,48 +15621,48 @@ 4: == unsigned int 4: == bool 4: == std::string -5: [12:00:54] +5: [09:20:23] 5: ----------------------------------------- -5: [12:00:54] Finished: testPushAndPop() -5: [12:00:54] +5: [09:20:23] Finished: testPushAndPop() +5: [09:20:23] 5: ----------------------------------------- -5: [12:00:54] +5: [09:20:23] 5: ----------------------------------------- -6: Randomness seeded to: 2613917016 +6: Randomness seeded to: 3477409277 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: -7: [12:00:54] should not be silent -7: [12:00:54] should not be silent -7: Randomness seeded to: 640667146 -7: [12:00:54] should not be silent -7: [12:00:54] should not be silent -7: [12:00:54] should not be silent -7: [12:00:54] should not be silent -7: [12:00:54] should not be silent -7: [12:00:54] should not be silent -7: [12:00:54] should not be silent -7: [12:00:54] should not be silent +7: [09:20:23] should not be silent +7: [09:20:23] should not be silent +7: Randomness seeded to: 1244189375 +7: [09:20:23] should not be silent +7: [09:20:23] should not be silent +7: [09:20:23] should not be silent +7: [09:20:23] should not be silent +7: [09:20:23] should not be silent +7: [09:20:23] should not be silent +7: [09:20:23] should not be silent +7: [09:20:23] should not be silent 7: =============================================================================== 7: All tests passed (26 assertions in 3 test cases) 7: -8: [12:00:54] pass -8: [12:00:54] v3 4 -8: [12:00:54] v4 5 -8: [12:00:54] SPARSE ----------------------------------- -8: [12:00:54] Set 10: 0 -8: [12:00:54] Set 11: 0 -8: [12:00:54] Set 14: 0 -8: [12:00:54] Set 10: 1 -8: [12:00:54] Get 14: 1 -8: [12:00:54] Num: 20 -8: [12:00:54] NumOn: 3 -8: [12:00:54] NumOff: 17 +8: [09:20:23] pass +8: [09:20:23] v3 4 +8: [09:20:23] v4 5 +8: [09:20:23] SPARSE ----------------------------------- +8: [09:20:23] Set 10: 0 +8: [09:20:23] Set 11: 0 +8: [09:20:23] Set 14: 0 +8: [09:20:23] Set 10: 1 +8: [09:20:23] Get 14: 1 +8: [09:20:23] Num: 20 +8: [09:20:23] NumOn: 3 +8: [09:20:23] NumOff: 17 8: 10, 11, 14, -8: [12:00:54] t2[19]: 0 -8: [12:00:54] t2[14]: 1 -8: [12:00:54] t2[19]: 0 -8: [12:00:54] t2[14]: 0 +8: [09:20:23] t2[19]: 0 +8: [09:20:23] t2[14]: 1 +8: [09:20:23] t2[19]: 0 +8: [09:20:23] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -15766,20 +15670,20 @@ 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except -8: [12:00:54] Explicit ---------------------------------- -8: [12:00:54] Set 10: 0 -8: [12:00:54] Set 11: 0 -8: [12:00:54] Set 14: 0 -8: [12:00:54] Set 10: 1 -8: [12:00:54] Get 14: 1 -8: [12:00:54] Num: 20 -8: [12:00:54] NumOn: 3 -8: [12:00:54] NumOff: 17 +8: [09:20:24] Explicit ---------------------------------- +8: [09:20:24] Set 10: 0 +8: [09:20:24] Set 11: 0 +8: [09:20:24] Set 14: 0 +8: [09:20:24] Set 10: 1 +8: [09:20:24] Get 14: 1 +8: [09:20:24] Num: 20 +8: [09:20:24] NumOn: 3 +8: [09:20:24] NumOff: 17 8: 10, 11, 14, -8: [12:00:54] t2[19]: 0 -8: [12:00:54] t2[14]: 1 -8: [12:00:54] t2[19]: 0 -8: [12:00:54] t2[14]: 0 +8: [09:20:24] t2[19]: 0 +8: [09:20:24] t2[14]: 1 +8: [09:20:24] t2[19]: 0 +8: [09:20:24] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -15787,34 +15691,34 @@ 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except -8: [12:00:54] Done -8: [12:00:54] Test DiscreteValue Vectors 1 ---------------------------- -8: [12:00:54] Expected failure: Value out of range -8: [12:00:54] Expected failure: Value out of range -8: [12:00:54] Expected failure: Value out of range -8: [12:00:54] Expected failure: Value out of range -8: [12:00:54] Expected failure: Value out of range -8: [12:00:54] Test DiscreteValue Vectors 2 ------------------------------ -8: [12:00:54] Test DiscreteValue Vectors 3 --------------------------- -8: [12:00:54] Test DiscreteValue Operations ----------------------------- -8: [12:00:54] Test DiscreteValue Operations 2 -------------------------- -8: [12:00:54] Test SparseIntVect ------------------------------------ -8: [12:00:54] Test SparseIntVect Serialization -------------------------- -8: [12:00:54] Test BitVect Serialization ------------------------------- -8: [12:00:54] Test BitVect to FPS ------------------------------- -8: [12:00:54] Test BitVect to binary string ------------------------------- -8: [12:00:54] Test Similarity Measures BitVect ------------------------------- -8: [12:00:54] Test Similarity Measures SparseBitVect ------------------------------- -8: [12:00:54] Test BitVect with all ones ------------------------------- -8: [12:00:54] Test Explicit BitVects: Concatenation Operation ------------------------------- -8: [12:00:54] Test bitmap operations ------------------------------- -8: [12:00:54] Test bitmaps as properties ------------------------------- -8: [12:00:54] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- -8: [12:00:54] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- -8: [12:00:54] Test RealValue Vectors 2: L1Norm ------------------------------- -8: [12:00:54] Test RealValue Vectors 3: Pickles ------------------------------- -8: [12:00:54] Test RealValue Vectors 4: Vector Operations ------------------------------- -11: Randomness seeded to: 1694086242 +8: [09:20:24] Done +8: [09:20:24] Test DiscreteValue Vectors 1 ---------------------------- +8: [09:20:24] Expected failure: Value out of range +8: [09:20:24] Expected failure: Value out of range +8: [09:20:24] Expected failure: Value out of range +8: [09:20:24] Expected failure: Value out of range +8: [09:20:24] Expected failure: Value out of range +8: [09:20:24] Test DiscreteValue Vectors 2 ------------------------------ +8: [09:20:24] Test DiscreteValue Vectors 3 --------------------------- +8: [09:20:24] Test DiscreteValue Operations ----------------------------- +8: [09:20:24] Test DiscreteValue Operations 2 -------------------------- +8: [09:20:24] Test SparseIntVect ------------------------------------ +8: [09:20:24] Test SparseIntVect Serialization -------------------------- +8: [09:20:24] Test BitVect Serialization ------------------------------- +8: [09:20:24] Test BitVect to FPS ------------------------------- +8: [09:20:24] Test BitVect to binary string ------------------------------- +8: [09:20:24] Test Similarity Measures BitVect ------------------------------- +8: [09:20:24] Test Similarity Measures SparseBitVect ------------------------------- +8: [09:20:24] Test BitVect with all ones ------------------------------- +8: [09:20:24] Test Explicit BitVects: Concatenation Operation ------------------------------- +8: [09:20:24] Test bitmap operations ------------------------------- +8: [09:20:24] Test bitmaps as properties ------------------------------- +8: [09:20:24] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- +8: [09:20:24] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- +8: [09:20:24] Test RealValue Vectors 2: L1Norm ------------------------------- +8: [09:20:24] Test RealValue Vectors 3: Pickles ------------------------------- +8: [09:20:24] Test RealValue Vectors 4: Vector Operations ------------------------------- +11: Randomness seeded to: 1303485717 11: =============================================================================== 11: All tests passed (3 assertions in 1 test case) 11: @@ -15826,8 +15730,8 @@ 17: testPointOps2D 17: **************************************** 17: test12D -17: ref1: 0.40425 4.27445 ref2: 4.21502 3.0991 -17: pt1: 0.997257 2.54126 pt2: 1.88187 3.45063 +17: ref1: 0.231287 2.57019 ref2: 3.55123 3.70583 +17: pt1: 4.74482 0.817228 pt2: 1.6811 1.02586 17: **************************************** 17: test23D 17: **************************************** @@ -15842,6 +15746,87 @@ 17: **************************************** 17: testFromQuaternion 17: **************************************** + 1/235 Test #3: testDict ............................... Passed 0.41 sec + 2/235 Test #4: testRDValue ............................ Passed 0.41 sec + 3/235 Test #6: dictTestsCatch ......................... Passed 0.35 sec + 4/235 Test #7: logTestsCatch .......................... Passed 0.34 sec + 5/235 Test #8: testDataStructs ........................ Passed 0.33 sec + 6/235 Test #9: testFPB ................................ Passed 0.31 sec + 7/235 Test #10: testMultiFPB ........................... Passed 0.28 sec + 8/235 Test #11: catchDataStructs ....................... Passed 0.26 sec + 9/235 Test #17: testTransforms ......................... Passed 0.15 sec +test 21 + Start 21: testPyGeometry + +21: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/testGeometry.py" +21: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Geometry/Wrap +21: Test timeout computed to be: 1500 +test 22 + Start 22: testMatrices + +22: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/testMatrices +22: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics +22: Test timeout computed to be: 1500 +test 23 + Start 23: testConrec + +23: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/testConrec +23: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics +23: Test timeout computed to be: 1500 +test 24 + Start 24: testAlignment + +24: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment/testAlignment +24: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment +24: Test timeout computed to be: 1500 +test 25 + Start 25: pyAlignment + +25: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/Wrap/testAlignment.py" +25: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap +25: Test timeout computed to be: 1500 +test 26 + Start 26: testOptimizer + +26: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/testOptimizer +26: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Numerics/Optimizer +26: Test timeout computed to be: 1500 +test 27 + Start 27: ForceFieldsCatch + +27: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/ForceFieldsCatch +27: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField +27: Test timeout computed to be: 1500 +test 28 + Start 28: testUFFForceField + +28: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/UFF/testUFFForceField +28: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/UFF +28: Test timeout computed to be: 1500 +test 29 + Start 29: testMMFFForceField + +29: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField +29: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/MMFF +29: Test timeout computed to be: 1500 +20: Randomness seeded to: 2005799584 +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: 18: *********************************************************** 18: Testing Grid 18: --------------------------------- @@ -15859,34 +15844,20 @@ 18: --------------------------------- 18: testUniformGridIndexing 18: -19: *********************************************************** -19: Testing RealValueGrid3D -19: --------------------------------- -19: test1UniformRealValueGrid3D -19: -19: --------------------------------- -19: test2UniformRealValueGrid3DPickling -19: -19: --------------------------------- -19: test3UniformRealValueGrid3DIndexing -19: -19: --------------------------------- -19: test4UniformRealValueGrid3DOps -19: -20: Randomness seeded to: 558987549 -20: =============================================================================== -20: All tests passed (50 assertions in 5 test cases) -20: -22: [12:00:54] ----------------------------------------- -22: [12:00:54] Testing RDNumerics: vectors and matrices Code -22: [12:00:54] --------------------------------------- -22: [12:00:54] test1Vector -22: [12:00:54] --------------------------------------- -22: [12:00:54] test2Matrix -22: [12:00:54] --------------------------------------- -22: [12:00:54] test3SquareMatrix -22: [12:00:54] --------------------------------------- -22: [12:00:54] test4SymmMatrix +22: [09:20:24] ----------------------------------------- +22: [09:20:24] Testing RDNumerics: vectors and matrices Code +22: [09:20:24] --------------------------------------- +22: [09:20:24] test1Vector +22: [09:20:24] --------------------------------------- +22: [09:20:24] test2Matrix +22: [09:20:24] --------------------------------------- +22: [09:20:24] test3SquareMatrix +22: [09:20:24] --------------------------------------- +22: [09:20:24] test4SymmMatrix +23: Randomness seeded to: 3385487968 +23: =============================================================================== +23: All tests passed (76 assertions in 3 test cases) +23: 24: ----------------------------------------- 24: Testing Alignment Code 24: --------------------------------------- @@ -15904,6 +15875,59 @@ 26: ------------------------------------- 26: Testing BFGS optimization. 26: done + 10/235 Test #18: testGrid ............................... Passed 0.30 sec + 11/235 Test #19: testRealValueGrid ...................... Passed 0.28 sec + 12/235 Test #20: geometryTestsCatch ..................... Passed 0.25 sec + 13/235 Test #22: testMatrices ........................... Passed 0.17 sec + 14/235 Test #23: testConrec ............................. Passed 0.15 sec + 15/235 Test #24: testAlignment .......................... Passed 0.13 sec + 16/235 Test #26: testOptimizer .......................... Passed 0.09 sec +test 30 + Start 30: pyForceFieldConstraints + +30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ForceField/Wrap/testConstraints.py" +30: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ForceField/Wrap +30: Test timeout computed to be: 1500 +test 31 + Start 31: testDistGeom + +31: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom/testDistGeom +31: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom +31: Test timeout computed to be: 1500 +test 32 + Start 32: pyDistGeom + +32: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DistGeom/Wrap/rough_test.py" +32: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DistGeom/Wrap +32: Test timeout computed to be: 1500 +test 33 + Start 33: graphmolTest1 + +33: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +33: Test timeout computed to be: 1500 +test 34 + Start 34: graphmolcpTest + +34: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolcpTest +34: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +34: Test timeout computed to be: 1500 +test 35 + Start 35: graphmolqueryTest + +35: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +35: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +35: Test timeout computed to be: 1500 +test 36 + Start 36: graphmolMolOpsTest + +36: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMolOpsTest +36: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +36: Test timeout computed to be: 1500 +27: Randomness seeded to: 3899715159 +27: =============================================================================== +27: All tests passed (20 assertions in 2 test cases) +27: 28: ------------------------------------- 28: Unit tests for force field basics. 28: done @@ -15950,482 +15974,14 @@ 28: done 28: ------------------------------------- 28: Unit tests for all UFF constraint terms. - 1/235 Test #3: testDict ............................... Passed 0.29 sec - 2/235 Test #4: testRDValue ............................ Passed 0.28 sec - 3/235 Test #6: dictTestsCatch ......................... Passed 0.26 sec - 4/235 Test #7: logTestsCatch .......................... Passed 0.25 sec - 5/235 Test #8: testDataStructs ........................ Passed 0.24 sec - 6/235 Test #9: testFPB ................................ Passed 0.24 sec - 7/235 Test #10: testMultiFPB ........................... Passed 0.23 sec - 8/235 Test #11: catchDataStructs ....................... Passed 0.22 sec - 9/235 Test #17: testTransforms ......................... Passed 0.19 sec - 10/235 Test #18: testGrid ............................... Passed 0.18 sec - 11/235 Test #19: testRealValueGrid ...................... Passed 0.18 sec - 12/235 Test #20: geometryTestsCatch ..................... Passed 0.18 sec - 13/235 Test #22: testMatrices ........................... Passed 0.16 sec - 14/235 Test #24: testAlignment .......................... Passed 0.14 sec - 15/235 Test #26: testOptimizer .......................... Passed 0.13 sec -test 43 - Start 43: resMolSupplierTest - -43: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest -43: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -43: Test timeout computed to be: 1500 -test 44 - Start 44: molBundleTest - -44: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/molBundleTest -44: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -44: Test timeout computed to be: 1500 -test 45 - Start 45: testSGroup - -45: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/testSGroup -45: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -45: Test timeout computed to be: 1500 -test 46 - Start 46: test-valgrind - -46: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/test-valgrind -46: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -46: Test timeout computed to be: 1500 -test 47 - Start 47: graphmolTestsCatch - -47: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -47: Test timeout computed to be: 1500 -test 48 - Start 48: graphmolOrganometallicsCatch - -48: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch -48: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -48: Test timeout computed to be: 1500 -test 49 - Start 49: graphmolSGroupCatch - -49: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolSGroupCatch -49: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -49: Test timeout computed to be: 1500 -test 50 - Start 50: graphmolAdjustQueryCatch - -50: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch -50: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -50: Test timeout computed to be: 1500 -test 51 - Start 51: chiralityTestsCatch - -51: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/chiralityTestsCatch -51: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -51: Test timeout computed to be: 1500 -test 52 - Start 52: canonTestsCatch - -52: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/canonTestsCatch -52: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -52: Test timeout computed to be: 1500 -test 53 - Start 53: moliteratorTestsCatch - -53: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/moliteratorTestsCatch -53: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -53: Test timeout computed to be: 1500 -test 54 - Start 54: queryTestsCatch - -54: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/queryTestsCatch -54: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -54: Test timeout computed to be: 1500 -test 55 - Start 55: molbundleTestsCatch - -55: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/molbundleTestsCatch -55: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -55: Test timeout computed to be: 1500 -test 56 - Start 56: pickleTestsCatch - -56: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/pickleTestsCatch -56: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -56: Test timeout computed to be: 1500 -test 57 - Start 57: tableTestsCatch - -57: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/tableTestsCatch -57: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -57: Test timeout computed to be: 1500 -23: Randomness seeded to: 2715932679 -23: =============================================================================== -23: All tests passed (76 assertions in 3 test cases) -23: - 16/235 Test #23: testConrec ............................. Passed 0.26 sec -27: Randomness seeded to: 3684811888 -27: =============================================================================== -27: All tests passed (20 assertions in 2 test cases) -27: - 17/235 Test #27: ForceFieldsCatch ....................... Passed 0.23 sec -29: ------------------------------------- -29: Official MMFF validation suite. -31: *********************************************************** -31: test1 -31: *********************************************************** -31: testIssue216 -31: Rows: 4 Columns: 4 -31: 0 1 1 1 -31: 1 0 1 1 -31: 1 1 0 1 -31: 1 1 1 0 -31: *********************************************************** -31: - 18/235 Test #31: testDistGeom ........................... Passed 0.20 sec -33: Atoms: -33: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: -33: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: -33: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: -33: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: -33: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: -33: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: -33: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: -33: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: arom?: 1 query: AtomAtomicNum -33: 8 22 Ti chg: 0 deg: 1 exp: N/A imp: N/A hyb: -33: Bonds: -33: 0 0->1 order: 1 -33: 1 1->2 order: 2 -33: 2 2->3 order: 1 -33: 3 0->4 order: 1 -33: 4 5->6 order: 3 -33: 5 6->7 order: 1 -33: 6 7->8 order: 2 -33: [12:00:54] -33: -33: **** -33: Pre-condition Violation -33: bond already exists -33: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp -33: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x000055D573C4002C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x000055D573C3A041 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x00007F5C53E33D68 in /lib/x86_64-linux-gnu/libc.so.6 -33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -33: 7# 0x000055D573C3A0E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [12:00:54] -33: -33: **** -33: Pre-condition Violation -33: bond already exists -33: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp -33: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x000055D573C2E2F8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x000055D573C3A041 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x00007F5C53E33D68 in /lib/x86_64-linux-gnu/libc.so.6 -33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -33: 7# 0x000055D573C3A0E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [12:00:54] -33: -33: **** -33: Pre-condition Violation -33: attempt to add self-bond -33: Violation occurred on line 498 in file ./Code/GraphMol/RWMol.cpp -33: Failed Expression: atomIdx1 != atomIdx2 -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x000055D573C2E4DE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x000055D573C3A041 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x00007F5C53E33D68 in /lib/x86_64-linux-gnu/libc.so.6 -33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -33: 7# 0x000055D573C3A0E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [12:00:54] -33: -33: **** -33: Pre-condition Violation -33: bond already exists -33: Violation occurred on line 419 in file ./Code/GraphMol/ROMol.cpp -33: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x000055D573C2E51B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x000055D573C3A041 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x00007F5C53E33D68 in /lib/x86_64-linux-gnu/libc.so.6 -33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -33: 7# 0x000055D573C3A0E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [12:00:54] -33: -33: **** -33: Pre-condition Violation -33: attempt to add self-bond -33: Violation occurred on line 417 in file ./Code/GraphMol/ROMol.cpp -33: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x000055D573C2E64E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x000055D573C3A041 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x00007F5C53E33D68 in /lib/x86_64-linux-gnu/libc.so.6 -33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -33: 7# 0x000055D573C3A0E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [12:00:54] Explicit valence for atom # 0 B, 4, is greater than permitted -33: [12:00:54] Explicit valence for atom # 0 B, 4, is greater than permitted -33: [12:00:54] -33: -33: **** -33: Post-condition Violation -33: Element 'Xx' not found -33: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -33: Failed Expression: anum > -1 -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x000055D573C62997 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x000055D573C4B4DD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x000055D573C3A050 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 6# 0x00007F5C53E33D68 in /lib/x86_64-linux-gnu/libc.so.6 -33: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -33: 8# 0x000055D573C3A0E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [12:00:54] ------------------------------------- -33: [12:00:54] Test github381: thread-safe initialization of the periodic table -33: [12:00:54] done -33: [12:00:54] ------------------------------------- -33: [12:00:54] Test github1041: Segfault for atom with no owner (expect some warnings) -33: [12:00:54] -33: -33: **** -33: Pre-condition Violation -33: no owner -33: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h -33: Failed Expression: dp_mol -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# 0x000055D573C58B9B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x000055D573C3A07D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x00007F5C53E33D68 in /lib/x86_64-linux-gnu/libc.so.6 -33: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -33: 6# 0x000055D573C3A0E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [12:00:54] -33: -33: **** -33: Pre-condition Violation -33: no owner -33: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h -33: Failed Expression: dp_mol -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# 0x000055D573C39979 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x000055D573C3A07D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x00007F5C53E33D68 in /lib/x86_64-linux-gnu/libc.so.6 -33: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -33: 6# 0x000055D573C3A0E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [12:00:54] done -33: [12:00:54] ------------------------------------- -33: [12:00:54] Test github1041: Segfault for atom with no owner (expect some warnings) -33: [12:00:54] -33: -33: **** -33: Pre-condition Violation -33: no owner -33: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h -33: Failed Expression: dp_mol -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# 0x000055D573C58B9B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x000055D573C3A082 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x00007F5C53E33D68 in /lib/x86_64-linux-gnu/libc.so.6 -33: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -33: 6# 0x000055D573C3A0E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [12:00:54] -33: -33: **** -33: Pre-condition Violation -33: no owner -33: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h -33: Failed Expression: dp_mol -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# 0x000055D573C39979 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x000055D573C3A082 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x00007F5C53E33D68 in /lib/x86_64-linux-gnu/libc.so.6 -33: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -33: 6# 0x000055D573C3A0E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [12:00:54] done -33: [12:00:54] ------------------------------------- -33: [12:00:54] Test github1453: RWMol.clear() should reset the numBonds count. -33: [12:00:54] done -33: [12:00:54] ------------------------------------- -33: [12:00:54] Test range-based for loops. -33: [12:00:54] done -33: [12:00:54] ------------------------------------- -33: [12:00:54] Test github1642: Atom index type is too low for big molecules. -34: -34: -34: -34: COPY - 19/235 Test #34: graphmolcpTest ......................... Passed 0.19 sec -35: [12:00:54] ---------------------- Test1 -35: [12:00:54] Done! -35: [12:00:54] ---------------------- Test2 -35: [12:00:54] Done! -35: [12:00:54] ---------------------- Test3 -35: [12:00:54] Done! -35: [12:00:54] ---------------------- Test4 -35: [12:00:54] Done! -35: [12:00:54] ---------------------- Test5 -35: [12:00:54] Done! -35: [12:00:54] Done! -35: [12:00:54] ---------------------- Test issue 2892580 -35: [12:00:54] Done! -35: [12:00:54] ---------------------- Test github issue 53: query molecules not matching [R] -35: [12:00:54] Done! -35: [12:00:54] ---------------------- Test queries using qualifiers instead of == -35: [12:00:54] Done! -35: [12:00:54] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -35: [12:00:54] Done! -35: [12:00:54] ---------------------- Test extra atom queries -35: [12:00:54] Done! -35: [12:00:54] ---------------------- Test extra bond queries -35: [12:00:54] Done! -35: [12:00:54] ---------------------- Test num heteroatom neighbor queries -35: [12:00:54] Done! -35: [12:00:54] ---------------------- Test atom type queries -35: [12:00:54] Done! -35: [12:00:54] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -35: [12:00:54] Done! -35: [12:00:54] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -35: [12:00:54] Done! - 20/235 Test #35: graphmolqueryTest ...................... Passed 0.18 sec -38: [12:00:54] ------------------------------------- -38: [12:00:54] Testing String Pickle Roundtrips. -38: [12:00:54] done -38: [12:00:54] ------------------------------------- -38: [12:00:54] Testing reading existing pickle file (v2). -39: [12:00:54] done - 21/235 Test #42: graphmolMemTest1 ....................... Passed 0.15 sec -test 58 - Start 58: molopsTestsCatch - -58: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/molopsTestsCatch -58: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol -58: Test timeout computed to be: 1500 -test 59 - Start 59: smiTest1 - -59: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 -59: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -59: Test timeout computed to be: 1500 -test 60 - Start 60: smiTest2 - -60: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 -60: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -60: Test timeout computed to be: 1500 -test 61 - Start 61: cxsmilesTest - -61: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest -61: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -61: Test timeout computed to be: 1500 -test 62 - Start 62: smaTest1 - -62: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 -62: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -62: Test timeout computed to be: 1500 -test 63 - Start 63: smiTestCatch - -63: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -63: Test timeout computed to be: 1500 -41: [12:00:54] Testing the hanoi sort -41: [12:00:54] populating vectors -36: 1 1 2 -36: 1 1 1 -36: 2 1 0.75 -36: path: 2 -36: [12:00:54] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -36: [12:00:54] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -36: [12:00:54] Explicit valence for atom # 0 B, 5, is greater than permitted -36: [12:00:54] Explicit valence for atom # 1 C, 5, is greater than permitted -36: [12:00:54] Explicit valence for atom # 1 C, 5, is greater than permitted -36: [12:00:54] Explicit valence for atom # 1 C, 5, is greater than permitted -36: [12:00:54] Explicit valence for atom # 1 Si, 7, is greater than permitted -37: -------------------------- -37: -------------------------- -37: C/C=C/C(C)Cl -37: [12:00:54] Conflicting single bond directions around double bond at index 2. -37: [12:00:54] BondStereo set to STEREONONE and single bond directions set to NONE. -37: [12:00:54] Conflicting single bond directions around double bond at index 4. -37: [12:00:54] BondStereo set to STEREONONE and single bond directions set to NONE. -37: [12:00:54] Conflicting single bond directions around double bond at index 15. -37: [12:00:54] BondStereo set to STEREONONE and single bond directions set to NONE. -37: [12:00:54] Conflicting single bond directions around double bond at index 2. -37: [12:00:54] BondStereo set to STEREONONE and single bond directions set to NONE. -37: [12:00:54] Conflicting single bond directions around double bond at index 1. -37: [12:00:54] BondStereo set to STEREONONE and single bond directions set to NONE. -37: -------------------------------------------------- 28: done 28: ------------------------------------- 28: Unit tests for copying UFF ForceFields. 28: done 28: ------------------------------------- 28: Unit test for UFF butane scan. +29: ------------------------------------- +29: Official MMFF validation suite. 1: cyclosporine a 1: RDKit 2D 1: @@ -16786,40 +16342,599 @@ 1: 30 11 1 0 1: M END 1: -47: Randomness seeded to: 2076878227 -47: [12:00:54] WARNING: not removing hydrogen atom without neighbors -47: [12:00:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [12:00:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [12:00:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [12:00:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [12:00:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [12:00:54] Explicit valence for atom # 1 N, 5, is greater than permitted -47: [12:00:54] Explicit valence for atom # 1 N, 6, is greater than permitted -47: [12:00:54] Explicit valence for atom # 1 N, 5, is greater than permitted -47: [12:00:54] Explicit valence for atom # 1 N, 5, is greater than permitted -47: [12:00:54] Explicit valence for atom # 2 O, 3, is greater than permitted -47: [12:00:54] Explicit valence for atom # 2 O, 3, is greater than permitted -47: [12:00:54] non-ring atom 2 marked aromatic -47: [12:00:54] non-ring atom 2 marked aromatic -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 1 2 3 -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 1 2 3 -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 -47: [12:00:54] Explicit valence for atom # 1 O, 3, is greater than permitted -47: [12:00:54] Explicit valence for atom # 4 F, 2, is greater than permitted -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 6 7 8 -47: [12:00:54] Explicit valence for atom # 1 C, 5, is greater than permitted -47: [12:00:54] WARNING: not removing hydrogen atom with dummy atom neighbors -47: [12:00:54] WARNING: not removing hydrogen atom with dummy atom neighbors -47: [12:00:54] WARNING: not removing hydrogen atom with wedged bond -47: [12:00:54] WARNING: not removing hydrogen atom without neighbors -47: [12:00:54] WARNING: not removing hydrogen atom without neighbors -47: [12:00:54] WARNING: not removing hydrogen atom without neighbors -47: [12:00:54] WARNING: not removing hydrogen atom without neighbors -47: [12:00:54] Unreasonable formal charge on atom # 0. -47: [12:00:54] +31: *********************************************************** +31: test1 +31: *********************************************************** +31: testIssue216 +31: Rows: 4 Columns: 4 +31: 0 1 1 1 +31: 1 0 1 1 +31: 1 1 0 1 +31: 1 1 1 0 +31: *********************************************************** +31: +33: Atoms: +33: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: +33: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: +33: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: +33: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: +33: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: +33: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: +33: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: +33: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: arom?: 1 query: AtomAtomicNum +33: 8 22 Ti chg: 0 deg: 1 exp: N/A imp: N/A hyb: +33: Bonds: +33: 0 0->1 order: 1 +33: 1 1->2 order: 2 +33: 2 2->3 order: 1 +33: 3 0->4 order: 1 +33: 4 5->6 order: 3 +33: 5 6->7 order: 1 +33: 6 7->8 order: 2 +33: [09:20:24] +33: +33: **** +33: Pre-condition Violation +33: bond already exists +33: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp +33: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +33: 3# 0x000055E8E0FEA02C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x000055E8E0FE4041 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x00007FFBAF22ED68 in /lib/x86_64-linux-gnu/libc.so.6 +33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +33: 7# 0x000055E8E0FE40E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [09:20:24] +33: +33: **** +33: Pre-condition Violation +33: bond already exists +33: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp +33: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +33: 3# 0x000055E8E0FD82F8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x000055E8E0FE4041 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x00007FFBAF22ED68 in /lib/x86_64-linux-gnu/libc.so.6 +33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +33: 7# 0x000055E8E0FE40E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [09:20:24] +33: +33: **** +33: Pre-condition Violation +33: attempt to add self-bond +33: Violation occurred on line 498 in file ./Code/GraphMol/RWMol.cpp +33: Failed Expression: atomIdx1 != atomIdx2 +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +33: 3# 0x000055E8E0FD84DE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x000055E8E0FE4041 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x00007FFBAF22ED68 in /lib/x86_64-linux-gnu/libc.so.6 +33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +33: 7# 0x000055E8E0FE40E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [09:20:24] +33: +33: **** +33: Pre-condition Violation +33: bond already exists +33: Violation occurred on line 419 in file ./Code/GraphMol/ROMol.cpp +33: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +33: 3# 0x000055E8E0FD851B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x000055E8E0FE4041 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x00007FFBAF22ED68 in /lib/x86_64-linux-gnu/libc.so.6 +33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +33: 7# 0x000055E8E0FE40E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [09:20:24] +33: +33: **** +33: Pre-condition Violation +33: attempt to add self-bond +33: Violation occurred on line 417 in file ./Code/GraphMol/ROMol.cpp +33: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +33: 3# 0x000055E8E0FD864E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x000055E8E0FE4041 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x00007FFBAF22ED68 in /lib/x86_64-linux-gnu/libc.so.6 +33: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +33: 7# 0x000055E8E0FE40E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [09:20:24] Explicit valence for atom # 0 B, 4, is greater than permitted +33: [09:20:24] Explicit valence for atom # 0 B, 4, is greater than permitted +33: [09:20:24] +33: +33: **** +33: Post-condition Violation +33: Element 'Xx' not found +33: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +33: Failed Expression: anum > -1 +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 3# 0x000055E8E100C997 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x000055E8E0FF54DD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x000055E8E0FE4050 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 6# 0x00007FFBAF22ED68 in /lib/x86_64-linux-gnu/libc.so.6 +33: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +33: 8# 0x000055E8E0FE40E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [09:20:24] ------------------------------------- +33: [09:20:24] Test github381: thread-safe initialization of the periodic table +34: +34: +34: +34: COPY +35: [09:20:24] ---------------------- Test1 +35: [09:20:24] Done! +35: [09:20:24] ---------------------- Test2 +35: [09:20:24] Done! +35: [09:20:24] ---------------------- Test3 +35: [09:20:24] Done! +35: [09:20:24] ---------------------- Test4 +35: [09:20:24] Done! +35: [09:20:24] ---------------------- Test5 +35: [09:20:24] Done! +35: [09:20:24] Done! +35: [09:20:24] ---------------------- Test issue 2892580 +35: [09:20:24] Done! +35: [09:20:24] ---------------------- Test github issue 53: query molecules not matching [R] +35: [09:20:24] Done! +35: [09:20:24] ---------------------- Test queries using qualifiers instead of == +35: [09:20:24] Done! +35: [09:20:24] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +35: [09:20:24] Done! +35: [09:20:24] ---------------------- Test extra atom queries +35: [09:20:24] Done! +35: [09:20:24] ---------------------- Test extra bond queries +35: [09:20:24] Done! +35: [09:20:24] ---------------------- Test num heteroatom neighbor queries +35: [09:20:24] Done! +35: [09:20:24] ---------------------- Test atom type queries +35: [09:20:24] Done! +35: [09:20:24] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +35: [09:20:24] Done! +35: [09:20:24] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +35: [09:20:24] Done! + 17/235 Test #27: ForceFieldsCatch ....................... Passed 0.34 sec + 18/235 Test #31: testDistGeom ........................... Passed 0.25 sec + 19/235 Test #34: graphmolcpTest ......................... Passed 0.18 sec + 20/235 Test #35: graphmolqueryTest ...................... Passed 0.11 sec +test 37 + Start 37: graphmoltestChirality + +37: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestChirality +37: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +37: Test timeout computed to be: 1500 +test 38 + Start 38: graphmoltestPickler + +38: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPickler +38: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +38: Test timeout computed to be: 1500 +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.086s +2: +2: OK +test 39 + Start 39: graphmoltestPicklerGlobalSetting + +39: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting +39: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +39: Test timeout computed to be: 1500 +test 40 + Start 40: graphmolIterTest + +40: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolIterTest +40: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +40: Test timeout computed to be: 1500 +33: [09:20:24] done +33: [09:20:24] ------------------------------------- +33: [09:20:24] Test github1041: Segfault for atom with no owner (expect some warnings) +33: [09:20:24] +33: +33: **** +33: Pre-condition Violation +33: no owner +33: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h +33: Failed Expression: dp_mol +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# 0x000055E8E1002B9B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 3# 0x000055E8E0FE407D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x00007FFBAF22ED68 in /lib/x86_64-linux-gnu/libc.so.6 +33: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +33: 6# 0x000055E8E0FE40E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [09:20:24] +33: +33: **** +33: Pre-condition Violation +33: no owner +33: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h +33: Failed Expression: dp_mol +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# 0x000055E8E0FE3979 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 3# 0x000055E8E0FE407D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x00007FFBAF22ED68 in /lib/x86_64-linux-gnu/libc.so.6 +33: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +33: 6# 0x000055E8E0FE40E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [09:20:24] done +33: [09:20:24] ------------------------------------- +33: [09:20:24] Test github1041: Segfault for atom with no owner (expect some warnings) +33: [09:20:24] +33: +33: **** +33: Pre-condition Violation +33: no owner +33: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h +33: Failed Expression: dp_mol +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# 0x000055E8E1002B9B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 3# 0x000055E8E0FE4082 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x00007FFBAF22ED68 in /lib/x86_64-linux-gnu/libc.so.6 +33: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +33: 6# 0x000055E8E0FE40E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [09:20:24] +33: +33: **** +33: Pre-condition Violation +33: no owner +33: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h +33: Failed Expression: dp_mol +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# 0x000055E8E0FE3979 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 3# 0x000055E8E0FE4082 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x00007FFBAF22ED68 in /lib/x86_64-linux-gnu/libc.so.6 +33: 5# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +33: 6# 0x000055E8E0FE40E1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [09:20:24] done +33: [09:20:24] ------------------------------------- +33: [09:20:24] Test github1453: RWMol.clear() should reset the numBonds count. +33: [09:20:24] done +33: [09:20:24] ------------------------------------- +33: [09:20:24] Test range-based for loops. +33: [09:20:24] done +33: [09:20:24] ------------------------------------- +33: [09:20:24] Test github1642: Atom index type is too low for big molecules. +36: 1 1 2 +36: 1 1 1 +36: 2 1 0.75 +36: path: 2 +36: [09:20:24] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +36: [09:20:24] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +36: [09:20:24] Explicit valence for atom # 0 B, 5, is greater than permitted +36: [09:20:24] Explicit valence for atom # 1 C, 5, is greater than permitted +36: [09:20:24] Explicit valence for atom # 1 C, 5, is greater than permitted +36: [09:20:24] Explicit valence for atom # 1 C, 5, is greater than permitted +36: [09:20:24] Explicit valence for atom # 1 Si, 7, is greater than permitted +14: ...... +14: ---------------------------------------------------------------------- +14: Ran 6 tests in 0.011s +14: +14: OK +38: [09:20:24] ------------------------------------- +38: [09:20:24] Testing String Pickle Roundtrips. +39: [09:20:24] done + 21/235 Test #39: graphmoltestPicklerGlobalSetting ....... Passed 0.07 sec +test 41 + Start 41: hanoiTest + +41: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest +41: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +41: Test timeout computed to be: 1500 +37: -------------------------- +37: -------------------------- +37: C/C=C/C(C)Cl + 22/235 Test #1: testCoordGen ........................... Passed 1.09 sec +test 42 + Start 42: graphmolMemTest1 + +42: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 +42: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +42: Test timeout computed to be: 1500 +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... + 23/235 Test #40: graphmolIterTest ....................... Passed 0.10 sec +test 43 + Start 43: resMolSupplierTest + +43: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest +43: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +43: Test timeout computed to be: 1500 + 24/235 Test #42: graphmolMemTest1 ....................... Passed 0.05 sec +test 44 + Start 44: molBundleTest + +44: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/molBundleTest +44: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +44: Test timeout computed to be: 1500 +15: ......... +15: ---------------------------------------------------------------------- +15: Ran 9 tests in 0.043s +15: +15: OK +41: [09:20:24] Testing the hanoi sort +41: [09:20:24] populating vectors +16: ......... +16: ---------------------------------------------------------------------- +16: Ran 9 tests in 0.105s +16: +16: OK + 25/235 Test #2: pyCoordGen ............................. Passed 1.17 sec +test 45 + Start 45: testSGroup + +45: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/testSGroup +45: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +45: Test timeout computed to be: 1500 +36: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 +38: [09:20:25] done +38: [09:20:25] ------------------------------------- +38: [09:20:25] Testing reading existing pickle file (v2). + 26/235 Test #44: molBundleTest .......................... Passed 0.10 sec +test 46 + Start 46: test-valgrind + +46: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/test-valgrind +46: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +46: Test timeout computed to be: 1500 +25: ..... +25: ---------------------------------------------------------------------- +25: Ran 5 tests in 0.008s +25: +25: OK +25: Testing Alignment Wrapper code: +37: [09:20:25] Conflicting single bond directions around double bond at index 2. +37: [09:20:25] BondStereo set to STEREONONE and single bond directions set to NONE. +37: [09:20:25] Conflicting single bond directions around double bond at index 4. +37: [09:20:25] BondStereo set to STEREONONE and single bond directions set to NONE. +37: [09:20:25] Conflicting single bond directions around double bond at index 15. +37: [09:20:25] BondStereo set to STEREONONE and single bond directions set to NONE. +37: [09:20:25] Conflicting single bond directions around double bond at index 2. +37: [09:20:25] BondStereo set to STEREONONE and single bond directions set to NONE. +37: [09:20:25] Conflicting single bond directions around double bond at index 1. +37: [09:20:25] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [09:20:25] non-ring atom 0 marked aromatic +36: [09:20:25] non-ring atom 0 marked aromatic + 27/235 Test #46: test-valgrind .......................... Passed 0.09 sec +test 47 + Start 47: graphmolTestsCatch + +47: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +47: Test timeout computed to be: 1500 +36: [09:20:25] Conflicting single bond directions around double bond at index 17. +36: [09:20:25] BondStereo set to STEREONONE and single bond directions set to NONE. + 28/235 Test #15: pySparseIntVect ........................ Passed 1.07 sec +test 48 + Start 48: graphmolOrganometallicsCatch + +48: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch +48: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +48: Test timeout computed to be: 1500 +38: [09:20:25] done +38: [09:20:25] ------------------------------------- +38: [09:20:25] Testing combining molecules using pickles. +38: Atoms: +38: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 +38: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 +38: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 +38: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 +38: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 +38: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: SP3 +38: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 +38: Bonds: +38: 0 0->1 order: 1 +38: 1 1->2 order: 1 +38: 2 2->0 order: 1 +38: 3 3->4 order: 1 +38: 4 4->5 order: 1 +38: 5 5->6 order: 1 +38: 6 6->3 order: 1 +38: [09:20:25] done +38: [09:20:25] ------------------------------------- +38: [09:20:25] Testing Issue164: Roundtrip Pickle Failure. +36: starting ring finding +36: done +36: starting ring finding + 29/235 Test #14: pyRealValueVect ........................ Passed 1.11 sec + 30/235 Test #16: pyFPB .................................. Passed 1.08 sec +36: done +36: starting ring finding +test 49 + Start 49: graphmolSGroupCatch + +49: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolSGroupCatch +49: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +49: Test timeout computed to be: 1500 +test 50 + Start 50: graphmolAdjustQueryCatch + +50: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch +50: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +50: Test timeout computed to be: 1500 +36: done +36: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C +36: starting sanitization +38: [09:20:25] done +38: [09:20:25] ------------------------------------- +38: [09:20:25] Testing Issue219: Pickle Failure with Conformations. +38: [09:20:25] done +38: [09:20:25] ------------------------------------- +38: [09:20:25] Testing Issue220: Pickle problems with bond stereochemistry. +38: [09:20:25] done +38: [09:20:25] ------------------------------------- +38: [09:20:25] Testing query serialization. +38: [09:20:25] C=[$(C=O)] +38: [09:20:25] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +38: [09:20:25] done +38: [09:20:25] ------------------------------------- +38: [09:20:25] Testing radical handling in pickles. +38: [09:20:25] done +38: [09:20:25] done +38: [09:20:25] ------------------------------------- +38: [09:20:25] Testing sf.net issue 2788233. +37: -------------------------------------------------- +47: Randomness seeded to: 1507803246 +47: [09:20:25] WARNING: not removing hydrogen atom without neighbors +47: [09:20:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [09:20:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [09:20:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. + 31/235 Test #25: pyAlignment ............................ Passed 0.86 sec +test 51 + Start 51: chiralityTestsCatch + +51: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/chiralityTestsCatch +51: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +51: Test timeout computed to be: 1500 +38: [09:20:25] done +38: [09:20:25] ------------------------------------- +38: [09:20:25] Testing sf.net issue 3202580. +38: mass! 13.0034 +38: [09:20:25] done +38: [09:20:25] ------------------------------------- +38: [09:20:25] Testing sf.net issue 3316407. +38: [09:20:25] done +38: [09:20:25] ------------------------------------- +38: [09:20:25] Testing sf.net issue 3496759. +38: smi match: *C *C +38: smi match: **=* **=* +38: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O +38: smi match: *OS(=O)OC *OS(=O)OC +38: smi match: *S(=O)(=O)OC *S(=O)(=O)OC +38: smi match: O=COC=O O=COC=O +38: smi match: OO OO +38: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F +47: [09:20:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [09:20:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [09:20:25] Explicit valence for atom # 1 N, 5, is greater than permitted +47: [09:20:25] Explicit valence for atom # 1 N, 6, is greater than permitted +47: [09:20:25] Explicit valence for atom # 1 N, 5, is greater than permitted +47: [09:20:25] Explicit valence for atom # 1 N, 5, is greater than permitted +47: [09:20:25] Explicit valence for atom # 2 O, 3, is greater than permitted +47: [09:20:25] Explicit valence for atom # 2 O, 3, is greater than permitted +47: [09:20:25] non-ring atom 2 marked aromatic +47: [09:20:25] non-ring atom 2 marked aromatic +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 1 2 3 +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 1 2 3 +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 +47: [09:20:25] Explicit valence for atom # 1 O, 3, is greater than permitted +47: [09:20:25] Explicit valence for atom # 4 F, 2, is greater than permitted +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 6 7 8 +47: [09:20:25] Explicit valence for atom # 1 C, 5, is greater than permitted +47: [09:20:25] WARNING: not removing hydrogen atom with dummy atom neighbors +47: [09:20:25] WARNING: not removing hydrogen atom with dummy atom neighbors +47: [09:20:25] WARNING: not removing hydrogen atom with wedged bond +47: [09:20:25] WARNING: not removing hydrogen atom without neighbors +47: [09:20:25] WARNING: not removing hydrogen atom without neighbors +13: ...... +13: ---------------------------------------------------------------------- +13: Ran 6 tests in 0.028s +13: +13: OK + 32/235 Test #37: graphmoltestChirality .................. Passed 0.51 sec +38: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 +38: smi match: nnnOC=O nnnOC=O +38: smi match: *=C=N *=C=N +47: [09:20:25] WARNING: not removing hydrogen atom without neighbors +47: [09:20:25] WARNING: not removing hydrogen atom without neighbors +36: done +test 52 + Start 52: canonTestsCatch + +52: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/canonTestsCatch +52: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +52: Test timeout computed to be: 1500 +38: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F +38: smi match: SP(S)=S SP(S)=S +38: smi match: NP(N)(N)=O NP(N)(N)=O +38: smi match: cN=[N+]=[N-] cN=[N+]=[N-] +38: smi match: *CC=O *CC=O +38: smi match: NNC=O NNC=O +38: smi match: * * +38: smi match: C=P C=P +38: smi match: CC(=N)Cl CC(=N)Cl +38: smi match: N=O N=O +38: smi match: ** ** +38: smi match: N=C=N N=C=N +38: smi match: [C-]#[NH+] [C-]#[NH+] +38: smi match: O=CON(C=O)C=O O=CON(C=O)C=O +38: smi match: N#CC[OH] N#CC[OH] +38: smi match: N#CC=O N#CC=O +38: smi match: N#CS(=O)=O N#CS(=O)=O +38: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC +38: smi match: N#CN=N N#CN=N +38: smi match: N=NCC=O N=NCC=O +38: smi match: CCCCCCC CCCCCCC +38: smi match: OCCOCCO OCCOCCO +38: smi match: SS SS +38: smi match: [SH] [SH] +38: smi match: *1CC1 *1CC1 +38: smi match: [OH]ccc([OH])c[OH] [OH]ccc([OH])c[OH] +47: [09:20:25] Unreasonable formal charge on atom # 0. +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -16831,20 +16946,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A85E798 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x0000560272021798 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -16856,20 +16971,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A85E822 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x0000560272021822 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -16881,20 +16996,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A85E8B5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x00005602720218B5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -16906,20 +17021,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A85E9A0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x00005602720219A0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -16931,20 +17046,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A85EA31 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x0000560272021A31 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -16956,20 +17071,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A85EACD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x0000560272021ACD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -16981,20 +17096,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A85F3E9 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x00005602720223E9 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -17006,22 +17121,45 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A85EC38 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x0000560272021C38 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] +47: [09:20:25] 47: 47: **** +36: starting sanitization +36: done +36: starting ring finding +36: done +36: starting ring finding +36: done +36: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 + 33/235 Test #45: testSGroup ............................. Passed 0.31 sec +38: smi match: [OH]cc([OH])c[OH] [OH]cc([OH])c[OH] +38: smi match: NC(=S)N=N NC(=S)N=N +38: smi match: N#CS N#CS +38: smi match: cC[N+] cC[N+] +38: smi match: C*C=S C*C=S +38: smi match: N[CH2]C#N N[CH2]C#N +38: smi match: O=C1CCO1 O=C1CCO1 +38: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH] +38: smi match: O=C1CCN1 O=C1CCN1 +38: smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1 +38: smi match: C=CC=CC=CC=C C=CC=CC=CC=C +38: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 +38: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 +38: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 +38: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 47: Pre-condition Violation 47: atom not associated with this molecule 47: Violation occurred on line 372 in file ./Code/GraphMol/ROMol.cpp @@ -17031,20 +17169,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A85ECD2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x0000560272021CD2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -17056,20 +17194,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A85F3C1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x00005602720223C1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -17081,20 +17219,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A85EFE8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x0000560272021FE8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -17106,24 +17244,24 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A85F39D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x000056027202239D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [12:00:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [12:00:54] WARNING: not removing hydrogen atom without neighbors -47: [12:00:54] Explicit valence for atom # 1 F greater than permitted -47: [12:00:54] +47: [09:20:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [09:20:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [09:20:25] WARNING: not removing hydrogen atom without neighbors +47: [09:20:25] Explicit valence for atom # 1 F greater than permitted +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -17135,20 +17273,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A807E4B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x0000560271FCAE4B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -17160,20 +17298,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A807EE0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x0000560271FCAEE0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -17185,20 +17323,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A807B70 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x0000560271FCAB70 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] +47: [09:20:25] 47: 47: **** 47: Pre-condition Violation @@ -17210,300 +17348,44 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x000055586A807C05 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x000055586A8ABAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x000055586A8AC5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x000055586A8ACA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x000055586A87E0C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x000055586A87E42C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x000055586A7FA46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x00007F243FC33D68 in /lib/x86_64-linux-gnu/libc.so.6 +47: 3# 0x0000560271FCAC05 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x000056027206EAB8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x000056027206F5D8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x000056027206FA50 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x00005602720410C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x000056027204142C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000560271FBD46E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x00007F69D1E2ED68 in /lib/x86_64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -47: 12# 0x000055586A7FA4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000560271FBD4B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [12:00:54] Unusual charge on atom 0 number of radical electrons set to zero -47: [12:00:54] Unusual charge on atom 0 number of radical electrons set to zero -47: [12:00:54] Unusual charge on atom 0 number of radical electrons set to zero -49: Randomness seeded to: 2712577241 +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [09:20:25] Unusual charge on atom 0 number of radical electrons set to zero +47: [09:20:25] Unusual charge on atom 0 number of radical electrons set to zero +47: [09:20:25] Unusual charge on atom 0 number of radical electrons set to zero +47: [09:20:25] non-ring atom 0 marked aromatic +47: [09:20:25] non-ring atom 0 marked aromatic +49: Randomness seeded to: 41934600 49: =============================================================================== 49: All tests passed (136 assertions in 8 test cases) 49: - 22/235 Test #39: graphmoltestPicklerGlobalSetting ....... Passed 0.20 sec - 23/235 Test #40: graphmolIterTest ....................... Passed 0.20 sec - 24/235 Test #44: molBundleTest .......................... Passed 0.15 sec - 25/235 Test #45: testSGroup ............................. Passed 0.15 sec - 26/235 Test #46: test-valgrind .......................... Passed 0.14 sec - 27/235 Test #49: graphmolSGroupCatch .................... Passed 0.12 sec -test 64 - Start 64: nontetrahedralCatch - -64: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch -64: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -64: Test timeout computed to be: 1500 -test 65 - Start 65: v2smiTestCatch - -65: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch -65: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -65: Test timeout computed to be: 1500 -test 66 - Start 66: testDepictor - -66: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor -66: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor -66: Test timeout computed to be: 1500 -test 67 - Start 67: depictorCatch - -67: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch -67: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor -67: Test timeout computed to be: 1500 -test 68 - Start 68: pyDepictor - -68: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/Wrap/testDepictor.py" -68: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap -68: Test timeout computed to be: 1500 -test 69 - Start 69: testMrvToMol + 34/235 Test #49: graphmolSGroupCatch .................... Passed 0.16 sec +test 53 + Start 53: moliteratorTestsCatch -69: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -69: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse -69: Test timeout computed to be: 1500 - 28/235 Test #37: graphmoltestChirality .................. Passed 0.26 sec -47: [12:00:54] non-ring atom 0 marked aromatic -47: [12:00:54] non-ring atom 0 marked aromatic -47: [12:00:54] Explicit valence for atom # 1 C, 5, is greater than permitted -47: [12:00:54] Explicit valence for atom # 9 C, 5, is greater than permitted -47: [12:00:54] Explicit valence for atom # 3 N, 4, is greater than permitted -47: [12:00:54] Explicit valence for atom # 15 C, 5, is greater than permitted -47: [12:00:54] Explicit valence for atom # 11 C, 5, is greater than permitted -47: [12:00:54] Explicit valence for atom # 9 C, 5, is greater than permitted -47: [12:00:54] Explicit valence for atom # 9 C, 5, is greater than permitted -47: [12:00:54] Explicit valence for atom # 9 C, 6, is greater than permitted -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 7 -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 3 -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 3 7 -47: [12:00:54] Can't kekulize mol. Unkekulized atoms: 3 7 -47: [12:00:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [12:00:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -53: Randomness seeded to: 3324028262 -53: =============================================================================== -53: All tests passed (14 assertions in 4 test cases) -53: - 29/235 Test #53: moliteratorTestsCatch .................. Passed 0.12 sec -54: Randomness seeded to: 3630021924 -54: =============================================================================== -54: All tests passed (10 assertions in 1 test case) -54: - 30/235 Test #54: queryTestsCatch ........................ Passed 0.12 sec -55: Randomness seeded to: 2224718382 -55: =============================================================================== -55: All tests passed (6 assertions in 1 test case) -55: - 31/235 Test #55: molbundleTestsCatch .................... Passed 0.11 sec -38: [12:00:54] done -38: [12:00:54] ------------------------------------- -38: [12:00:54] Testing combining molecules using pickles. -38: Atoms: -38: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 -38: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 -38: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 -38: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 -38: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 -38: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: SP3 -38: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 -38: Bonds: -38: 0 0->1 order: 1 -38: 1 1->2 order: 1 -38: 2 2->0 order: 1 -38: 3 3->4 order: 1 -38: 4 4->5 order: 1 -38: 5 5->6 order: 1 -38: 6 6->3 order: 1 -38: [12:00:54] done -38: [12:00:54] ------------------------------------- -38: [12:00:54] Testing Issue164: Roundtrip Pickle Failure. -38: [12:00:54] done -38: [12:00:54] ------------------------------------- -38: [12:00:54] Testing Issue219: Pickle Failure with Conformations. -38: [12:00:54] done -38: [12:00:54] ------------------------------------- -38: [12:00:54] Testing Issue220: Pickle problems with bond stereochemistry. -38: [12:00:54] done -38: [12:00:54] ------------------------------------- -38: [12:00:54] Testing query serialization. -38: [12:00:54] C=[$(C=O)] -38: [12:00:54] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -38: [12:00:54] done -38: [12:00:54] ------------------------------------- -38: [12:00:54] Testing radical handling in pickles. -38: [12:00:54] done -38: [12:00:54] done -38: [12:00:54] ------------------------------------- -38: [12:00:54] Testing sf.net issue 2788233. -38: [12:00:55] done -38: [12:00:55] ------------------------------------- -38: [12:00:55] Testing sf.net issue 3202580. -38: mass! 13.0034 -38: [12:00:55] done -38: [12:00:55] ------------------------------------- -38: [12:00:55] Testing sf.net issue 3316407. -38: [12:00:55] done -38: [12:00:55] ------------------------------------- -38: [12:00:55] Testing sf.net issue 3496759. -38: smi match: *C *C -38: smi match: **=* **=* -38: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O -38: smi match: *OS(=O)OC *OS(=O)OC -38: smi match: *S(=O)(=O)OC *S(=O)(=O)OC -38: smi match: O=COC=O O=COC=O -38: smi match: OO OO -38: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F -38: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 -38: smi match: nnnOC=O nnnOC=O -38: smi match: *=C=N *=C=N -38: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F -38: smi match: SP(S)=S SP(S)=S -38: smi match: NP(N)(N)=O NP(N)(N)=O -38: smi match: cN=[N+]=[N-] cN=[N+]=[N-] -38: smi match: *CC=O *CC=O -38: smi match: NNC=O NNC=O -38: smi match: * * -38: smi match: C=P C=P -38: smi match: CC(=N)Cl CC(=N)Cl -38: smi match: N=O N=O -38: smi match: ** ** -38: smi match: N=C=N N=C=N -38: smi match: [C-]#[NH+] [C-]#[NH+] -38: smi match: O=CON(C=O)C=O O=CON(C=O)C=O -38: smi match: N#CC[OH] N#CC[OH] -38: smi match: N#CC=O N#CC=O -38: smi match: N#CS(=O)=O N#CS(=O)=O -38: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC -38: smi match: N#CN=N N#CN=N -38: smi match: N=NCC=O N=NCC=O -38: smi match: CCCCCCC CCCCCCC -38: smi match: OCCOCCO OCCOCCO -38: smi match: SS SS -38: smi match: [SH] [SH] -38: smi match: *1CC1 *1CC1 -38: smi match: [OH]ccc([OH])c[OH] [OH]ccc([OH])c[OH] -38: smi match: [OH]cc([OH])c[OH] [OH]cc([OH])c[OH] -38: smi match: NC(=S)N=N NC(=S)N=N -38: smi match: N#CS N#CS -38: smi match: cC[N+] cC[N+] -38: smi match: C*C=S C*C=S -38: smi match: N[CH2]C#N N[CH2]C#N -38: smi match: O=C1CCO1 O=C1CCO1 -38: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH] -38: smi match: O=C1CCN1 O=C1CCN1 -38: smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1 -38: smi match: C=CC=CC=CC=C C=CC=CC=CC=C -38: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 -38: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 -38: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 -38: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 +53: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/moliteratorTestsCatch +53: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +53: Test timeout computed to be: 1500 38: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 38: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 38: smi match: cN(=O)~O cN(=O)~O 38: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O -56: Randomness seeded to: 2374226002 -56: =============================================================================== -56: All tests passed (45 assertions in 4 test cases) -56: - 32/235 Test #56: pickleTestsCatch ....................... Passed 0.11 sec -50: Randomness seeded to: 3947422207 -50: =============================================================================== -50: All tests passed (283 assertions in 11 test cases) -50: - 33/235 Test #50: graphmolAdjustQueryCatch ............... Passed 0.15 sec -51: Randomness seeded to: 3269134132 -51: [12:00:54] unable to set wavy bonds for double bonds: 3 -57: Randomness seeded to: 2293869473 -57: =============================================================================== -57: All tests passed (7 assertions in 2 test cases) -57: - 34/235 Test #57: tableTestsCatch ........................ Passed 0.10 sec -48: Randomness seeded to: 3820477331 -48: =============================================================================== -48: All tests passed (62 assertions in 6 test cases) -48: -60: [12:00:54] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -60: [12:00:54] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -60: [12:00:54] SMILES Parse Error: syntax error while parsing: - -60: [12:00:54] SMILES Parse Error: check for mistakes around position 1: -60: [12:00:54] - -60: [12:00:54] ^ -60: [12:00:54] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -60: [12:00:54] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -60: [12:00:54] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -60: [12:00:54] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -60: [12:00:54] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -60: [12:00:54] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -60: [12:00:54] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -60: [12:00:54] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -60: [12:00:54] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -60: [12:00:54] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -60: [12:00:54] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -60: [12:00:54] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 35/235 Test #60: smiTest2 ............................... Passed 0.07 sec -test 70 - Start 70: fileParsersTest1 - -70: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -70: Test timeout computed to be: 1500 -test 71 - Start 71: testAtropisomers - -71: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers -71: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -71: Test timeout computed to be: 1500 -test 72 - Start 72: testSquiggleDoubleBonds - -72: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds -72: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -72: Test timeout computed to be: 1500 -test 73 - Start 73: testMolSupplier - -73: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -73: Test timeout computed to be: 1500 -test 74 - Start 74: testGeneralFileReader - -74: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -74: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -74: Test timeout computed to be: 1500 -test 75 - Start 75: testMultithreadedMolSupplier - -75: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier -75: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -75: Test timeout computed to be: 1500 -test 76 - Start 76: testMolWriter - -76: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter -76: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -76: Test timeout computed to be: 1500 -test 77 - Start 77: testTplParser - -77: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser -77: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -77: Test timeout computed to be: 1500 38: smi match: N~NC=O N~NC=O 38: smi match: *=N~C *=N~C 38: smi match: CO*(=O)=O CO*(=O)=O @@ -17511,6 +17393,29 @@ 38: smi match: * * 38: smi match: *C=C *C=C 38: smi match: N#CS N#CS +47: [09:20:25] Explicit valence for atom # 1 C, 5, is greater than permitted +47: [09:20:25] Explicit valence for atom # 9 C, 5, is greater than permitted +47: [09:20:25] Explicit valence for atom # 3 N, 4, is greater than permitted +47: [09:20:25] Explicit valence for atom # 15 C, 5, is greater than permitted +47: [09:20:25] Explicit valence for atom # 11 C, 5, is greater than permitted +47: [09:20:25] Explicit valence for atom # 9 C, 5, is greater than permitted +47: [09:20:25] Explicit valence for atom # 9 C, 5, is greater than permitted +47: [09:20:25] Explicit valence for atom # 9 C, 6, is greater than permitted +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 7 +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 3 +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 3 7 +47: [09:20:25] Can't kekulize mol. Unkekulized atoms: 3 7 +47: [09:20:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [09:20:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +test 54 + Start 54: queryTestsCatch + +54: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/queryTestsCatch +54: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +54: Test timeout computed to be: 1500 +28: done + 35/235 Test #28: testUFFForceField ...................... Passed 0.96 sec 38: smi match: *C=S *C=S 38: smi match: *N *N 38: smi match: *C(=C)C=O *C(=C)C=O @@ -17522,6 +17427,20 @@ 38: smi match: C=C(C=O)C=O C=C(C=O)C=O 38: smi match: N=CC=O N=CC=O 38: smi match: *C(C=O)C=O *C(C=O)C=O +test 55 + Start 55: molbundleTestsCatch + +55: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/molbundleTestsCatch +55: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +55: Test timeout computed to be: 1500 +36: [09:20:25] WARNING: not removing hydrogen atom with dummy atom neighbors +36: ------------------------------- +36: [09:20:25] Explicit valence for atom # 0 N, 4, is greater than permitted +48: Randomness seeded to: 1242984741 +48: =============================================================================== +48: All tests passed (62 assertions in 6 test cases) +48: + 36/235 Test #48: graphmolOrganometallicsCatch ........... Passed 0.24 sec 38: smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O 38: smi match: O=CC=CC=O O=CC=CC=O 38: smi match: O=CN(O)C=O O=CN(O)C=O @@ -17530,6 +17449,14 @@ 38: smi match: O=CNN=O O=CNN=O 38: smi match: O=CNNC=O O=CNNC=O 38: smi match: O=CNOC=O O=CNOC=O +test 56 + Start 56: pickleTestsCatch + +56: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/pickleTestsCatch +56: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +56: Test timeout computed to be: 1500 +51: Randomness seeded to: 4196578443 +51: [09:20:25] unable to set wavy bonds for double bonds: 3 38: smi match: O=CS O=CS 38: smi match: O=CSC=S O=CSC=S 38: smi match: S=CS S=CS @@ -17538,6 +17465,16 @@ 38: smi match: CCCCCCC CCCCCCC 38: smi match: CN=O CN=O 38: smi match: CS(=O)(=O)O CS(=O)(=O)O +54: Randomness seeded to: 3494633958 +54: =============================================================================== +54: All tests passed (10 assertions in 1 test case) +54: +53: Randomness seeded to: 1014204390 +53: =============================================================================== +53: All tests passed (14 assertions in 4 test cases) +53: + 37/235 Test #53: moliteratorTestsCatch .................. Passed 0.10 sec + 38/235 Test #54: queryTestsCatch ........................ Passed 0.07 sec 38: smi match: O=C1CCO1 O=C1CCO1 38: smi match: C=C(S)[SH]=O C=C(S)[SH]=O 38: smi match: C=CCO C=CCO @@ -17551,6 +17488,31 @@ 38: smi match: *N(*)C=C *N(*)C=C 38: smi match: C=CN(=O)=O C=CN(=O)=O 38: smi match: C=CN(O)=O C=CN(O)=O +36: [09:20:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +36: [09:20:25] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +36: [09:20:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +36: [09:20:25] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: [09:20:25] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: [09:20:25] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: [09:20:25] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: [09:20:25] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: +test 57 + Start 57: tableTestsCatch + +57: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/tableTestsCatch +57: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +57: Test timeout computed to be: 1500 +test 58 + Start 58: molopsTestsCatch + +58: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/molopsTestsCatch +58: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol +58: Test timeout computed to be: 1500 +50: Randomness seeded to: 1333037174 +50: =============================================================================== +50: All tests passed (283 assertions in 11 test cases) +50: 38: smi match: C=CO C=CO 38: smi match: C=COC=O C=COC=O 38: smi match: C=CS C=CS @@ -17566,6 +17528,41 @@ 38: smi match: *CN=O *CN=O 38: smi match: NCN NCN 38: smi match: ON=CCN=O ON=CCN=O +51: [09:20:25] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +51: [09:20:25] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +47: [09:20:25] Explicit valence for atom # 1 O, 3, is greater than permitted +47: [09:20:25] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +47: [09:20:25] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +47: [09:20:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [09:20:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [09:20:25] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. +47: [09:20:25] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom +47: [09:20:25] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom +47: [09:20:25] non-ring atom 0 marked aromatic +55: Randomness seeded to: 448643869 +55: =============================================================================== +55: All tests passed (6 assertions in 1 test case) +55: +57: Randomness seeded to: 1846139426 +57: =============================================================================== +57: All tests passed (7 assertions in 2 test cases) +57: + 39/235 Test #50: graphmolAdjustQueryCatch ............... Passed 0.28 sec + 40/235 Test #55: molbundleTestsCatch .................... Passed 0.09 sec +test 59 + Start 59: smiTest1 + +59: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 +59: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +59: Test timeout computed to be: 1500 +test 60 + Start 60: smiTest2 + +60: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 +60: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +60: Test timeout computed to be: 1500 +47: [09:20:25] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +47: [09:20:25] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 38: smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O 38: smi match: N=C(N)S N=C(N)S 38: smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1 @@ -17579,6 +17576,38 @@ 38: smi match: N=C(N)O N=C(N)O 38: smi match: N=C(N)C(=N)S N=C(N)C(=N)S 38: smi match: *C=N *C=N + 41/235 Test #13: pyDiscreteValueVect .................... Passed 1.47 sec + 42/235 Test #57: tableTestsCatch ........................ Passed 0.08 sec +test 61 + Start 61: cxsmilesTest + +61: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest +61: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +61: Test timeout computed to be: 1500 +test 62 + Start 62: smaTest1 + +62: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 +62: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +62: Test timeout computed to be: 1500 +21: .................... +21: ---------------------------------------------------------------------- +21: Ran 20 tests in 0.368s +21: +21: OK +21: Testing Geometry wrapper +56: Randomness seeded to: 583919672 +56: =============================================================================== +56: All tests passed (45 assertions in 4 test cases) +56: + 43/235 Test #56: pickleTestsCatch ....................... Passed 0.15 sec +36: [09:20:25] WARNING: not removing hydrogen atom with dummy atom neighbors +test 63 + Start 63: smiTestCatch + +63: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +63: Test timeout computed to be: 1500 38: smi match: N=CC=O N=CC=O 38: smi match: N=CS N=CS 38: smi match: N=C=N N=C=N @@ -17618,61 +17647,6 @@ 38: smi match: SC(S)(S)S SC(S)(S)S 38: smi match: OS(O)(O)O OS(O)(O)O 38: smi match: O=N(=O)C[SH](=O)=O O=N(=O)C[SH](=O)=O - 36/235 Test #48: graphmolOrganometallicsCatch ........... Passed 0.22 sec -36: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 -36: [12:00:55] non-ring atom 0 marked aromatic -36: [12:00:55] non-ring atom 0 marked aromatic -36: [12:00:55] Conflicting single bond directions around double bond at index 17. -36: [12:00:55] BondStereo set to STEREONONE and single bond directions set to NONE. -36: starting ring finding -36: done -36: starting ring finding -36: done -36: starting ring finding -58: Randomness seeded to: 1350101589 -58: =============================================================================== -58: All tests passed (79 assertions in 6 test cases) -58: - 37/235 Test #58: molopsTestsCatch ....................... Passed 0.14 sec - 38/235 Test #1: testCoordGen ........................... Passed 0.56 sec -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... -59: [12:00:55] WARNING: not removing hydrogen atom without neighbors -59: [12:00:55] WARNING: not removing hydrogen atom without neighbors -59: [12:00:55] WARNING: not removing hydrogen atom without neighbors -59: [12:00:55] WARNING: not removing hydrogen atom without neighbors -59: [12:00:55] WARNING: not removing hydrogen atom without neighbors -59: [12:00:55] WARNING: not removing hydrogen atom without neighbors -59: [12:00:55] WARNING: not removing hydrogen atom without neighbors -59: [12:00:55] WARNING: not removing hydrogen atom without neighbors -59: [12:00:55] WARNING: not removing hydrogen atom without neighbors -59: [12:00:55] WARNING: not removing hydrogen atom without neighbors -59: [12:00:55] WARNING: not removing hydrogen atom without neighbors -59: [12:00:55] Invalid chiral specification on atom 0 -59: [12:00:55] Invalid chiral specification on atom 0 -59: [12:00:55] Invalid chiral specification on atom 0 -59: [12:00:55] Invalid chiral specification on atom 0 -59: [12:00:55] Invalid chiral specification on atom 0 -59: [12:00:55] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -59: [12:00:55] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -test 78 - Start 78: testMol2ToMol - -78: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol -78: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -78: Test timeout computed to be: 1500 -test 79 - Start 79: testSequence - -79: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence -79: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -79: Test timeout computed to be: 1500 -test 80 - Start 80: testExtendedStereoParsing - -80: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing -80: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -80: Test timeout computed to be: 1500 38: smi match: O=N(O)C[SH](=O)=O O=N(O)C[SH](=O)=O 38: smi match: N#CS N#CS 38: smi match: C=NO C=NO @@ -17683,6 +17657,78 @@ 38: smi match: O=N=O O=N=O 38: smi match: O=NO O=NO 38: smi match: ONO ONO +51: [09:20:25] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +51: [09:20:25] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +51: [09:20:25] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +51: =============================================================================== +51: All tests passed (2267 assertions in 79 test cases) +51: +47: [09:20:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [09:20:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [09:20:25] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +60: [09:20:25] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +60: [09:20:25] SMILES Parse Error: syntax error while parsing: - +60: [09:20:25] SMILES Parse Error: check for mistakes around position 1: +60: [09:20:25] - +60: [09:20:25] ^ +60: [09:20:25] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +60: [09:20:25] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +60: [09:20:25] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +60: [09:20:25] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +60: [09:20:25] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +60: [09:20:25] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +60: [09:20:25] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +60: [09:20:25] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +60: [09:20:25] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +60: [09:20:25] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +60: [09:20:25] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +60: [09:20:25] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' +58: Randomness seeded to: 3348049246 +58: =============================================================================== +58: All tests passed (79 assertions in 6 test cases) +58: + 44/235 Test #60: smiTest2 ............................... Passed 0.10 sec +test 64 + Start 64: nontetrahedralCatch + +64: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch +64: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +64: Test timeout computed to be: 1500 + 45/235 Test #51: chiralityTestsCatch .................... Passed 0.41 sec + 46/235 Test #58: molopsTestsCatch ....................... Passed 0.17 sec +59: [09:20:25] WARNING: not removing hydrogen atom without neighbors +59: [09:20:25] WARNING: not removing hydrogen atom without neighbors +59: [09:20:25] WARNING: not removing hydrogen atom without neighbors +59: [09:20:25] WARNING: not removing hydrogen atom without neighbors +59: [09:20:25] WARNING: not removing hydrogen atom without neighbors +59: [09:20:25] WARNING: not removing hydrogen atom without neighbors +59: [09:20:25] WARNING: not removing hydrogen atom without neighbors +59: [09:20:25] WARNING: not removing hydrogen atom without neighbors +59: [09:20:25] WARNING: not removing hydrogen atom without neighbors +59: [09:20:25] WARNING: not removing hydrogen atom without neighbors +59: [09:20:25] WARNING: not removing hydrogen atom without neighbors +59: [09:20:25] Invalid chiral specification on atom 0 +59: [09:20:25] Invalid chiral specification on atom 0 +59: [09:20:25] Invalid chiral specification on atom 0 +59: [09:20:25] Invalid chiral specification on atom 0 +59: [09:20:25] Invalid chiral specification on atom 0 +30: ...[09:20:25] Molecule does not have explicit Hs. Consider calling AddHs() +test 65 + Start 65: v2smiTestCatch + +65: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch +65: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +65: Test timeout computed to be: 1500 +test 66 + Start 66: testDepictor + +66: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor +66: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor +66: Test timeout computed to be: 1500 +47: [09:20:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [09:20:25] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +47: [09:20:25] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +47: [09:20:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 38: smi match: C1SCS1 C1SCS1 38: smi match: N=C=S N=C=S 38: smi match: N=C=N N=C=N @@ -17707,6 +17753,8 @@ 38: smi match: ONO ONO 38: smi match: ON(~O)~O ON(~O)~O 38: smi match: OC1COC(O)C1 OC1COC(O)C1 +47: [09:20:25] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +47: [09:20:25] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 38: smi match: OC1CCOC1O OC1CCOC1O 38: smi match: OC1CCOC(O)C1 OC1CCOC(O)C1 38: smi match: N=[N+]=N N=[N+]=N @@ -17720,6 +17768,16 @@ 38: smi match: COS(C)(=O)=O COS(C)(=O)=O 38: smi match: C1CO1 C1CO1 38: smi match: *c1-c-c-ccN1 *c1-c-c-ccN1 +59: [09:20:25] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +59: [09:20:25] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +47: [09:20:25] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +47: [09:20:25] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +63: Randomness seeded to: 1135831798 +63: [09:20:25] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +63: [09:20:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +63: [09:20:25] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +63: [09:20:25] SMARTS Parse Error: unclosed ring for input: 'C1C' +47: [09:20:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 38: smi match: *C(*)=C *C(*)=C 38: smi match: N#[NH+] N#[NH+] 38: smi match: C#NO C#NO @@ -17735,6 +17793,23 @@ 38: smi match: *C(*)(*)C=C *C(*)(*)C=C 38: smi match: *C(*)C=C *C(*)C=C 38: smi match: *CC=C *CC=C +63: [09:20:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +63: [09:20:25] SMARTS Parse Error: syntax error while parsing: C)foo +63: [09:20:25] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +63: [09:20:25] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +63: [09:20:25] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +63: [09:20:25] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +65: Randomness seeded to: 1574862051 +65: =============================================================================== +65: All tests passed (14 assertions in 2 test cases) +65: + 47/235 Test #65: v2smiTestCatch ......................... Passed 0.09 sec +test 67 + Start 67: depictorCatch + +67: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch +67: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor +67: Test timeout computed to be: 1500 38: smi match: CN=C=O CN=C=O 38: smi match: CN=C=S CN=C=S 38: smi match: *C=O *C=O @@ -17747,54 +17822,14 @@ 38: smi match: *C(=O)OC=O *C(=O)OC=O 38: smi match: C=CC#N C=CC#N 38: smi match: C=CC=O C=CC=O +32: ...... +32: ---------------------------------------------------------------------- +32: Ran 6 tests in 0.002s +32: +32: OK 38: smi match: CC=CC(C)=O CC=CC(C)=O 38: smi match: CC=CC(=O)OCC CC=CC(=O)OCC 38: smi match: C#CC#N C#CC#N -51: [12:00:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -51: [12:00:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -51: [12:00:55] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -51: [12:00:55] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -51: [12:00:55] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored -51: =============================================================================== -51: All tests passed (2267 assertions in 79 test cases) -51: -64: Randomness seeded to: 2811833177 -64: [12:00:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [12:00:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [12:00:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [12:00:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [12:00:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [12:00:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [12:00:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [12:00:55] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -65: Randomness seeded to: 2017603416 -65: =============================================================================== -65: All tests passed (14 assertions in 2 test cases) -65: -63: Randomness seeded to: 2960889669 -63: [12:00:55] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -63: [12:00:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -63: [12:00:55] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -63: [12:00:55] SMARTS Parse Error: unclosed ring for input: 'C1C' -63: [12:00:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -63: [12:00:55] SMARTS Parse Error: syntax error while parsing: C)foo -63: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -63: [12:00:55] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -63: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -63: [12:00:55] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -13: ...... -13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.030s -13: -13: OK -71: [12:00:55] ---- Running with POSIX locale ----- - 39/235 Test #65: v2smiTestCatch ......................... Passed 0.12 sec -test 81 - Start 81: fileParsersCatchTest - -81: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -81: Test timeout computed to be: 1500 38: smi match: C#CC=O C#CC=O 38: smi match: C#CC(=O)OCC C#CC(=O)OCC 38: smi match: C#CC=O C#CC=O @@ -17805,41 +17840,11 @@ 38: smi match: CS(=O)(=O)[O-] CS(=O)(=O)[O-] 38: smi match: NS(=O)(=O)[O-] NS(=O)(=O)[O-] 38: smi match: *C(*)(*)C=O *C(*)(*)C=O +64: Randomness seeded to: 796348517 +64: [09:20:25] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 38: smi match: *C(*)(*)C=O *C(*)(*)C=O 38: smi match: *C(*)C=O *C(*)C=O 38: smi match: *CC=O *CC=O - 40/235 Test #51: chiralityTestsCatch .................... Passed 0.24 sec -36: done -36: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C -36: starting sanitization -36: done -36: starting sanitization -73: [12:00:55] -73: ----------------------------------------- -74: [12:00:55] -74: ----------------------------------------- -74: [12:00:55] Finished: testDetermineFormat() -74: [12:00:55] ----------------------------------------- -74: -74: [12:00:55] -74: ----------------------------------------- -75: [12:00:55] -75: ----------------------------------------- -14: ...... -14: ---------------------------------------------------------------------- -14: Ran 6 tests in 0.006s -14: -14: OK -72: Randomness seeded to: 751578820 -72: =============================================================================== -72: All tests passed (15 assertions in 3 test cases) -72: -test 82 - Start 82: testPropertyLists - -82: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists -82: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -82: Test timeout computed to be: 1500 38: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 38: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 38: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O @@ -17853,41 +17858,6 @@ 38: smi match: N~[SiH4] N~[SiH4] 38: smi match: *P *P 38: smi match: C=N=N C=N=N -25: ..... -25: ---------------------------------------------------------------------- -25: Ran 5 tests in 0.006s -25: -25: OK -25: Testing Alignment Wrapper code: - 41/235 Test #72: testSquiggleDoubleBonds ................ Passed 0.08 sec -test 83 - Start 83: XYZFileParserCatchTest - -83: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest -83: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -83: Test timeout computed to be: 1500 -64: [12:00:55] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -64: =============================================================================== -64: All tests passed (308 assertions in 9 test cases) -64: - 42/235 Test #64: nontetrahedralCatch .................... Passed 0.15 sec -36: done -36: starting ring finding -36: done -36: starting ring finding -36: done -36: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 -15: ......... -15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.021s -15: -15: OK -test 84 - Start 84: cdxmlParserCatchTest - -84: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest -84: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -84: Test timeout computed to be: 1500 38: smi match: *N#[NH+] *N#[NH+] 38: smi match: *S* *S* 38: smi match: ** ** @@ -17916,45 +17886,26 @@ 38: smi match: *C* *C* 38: smi match: * * 38: smi match: C[nH3+] C[nH3+] +62: [09:20:25] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +62: [09:20:25] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +62: [09:20:25] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +62: [09:20:25] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' 38: smi match: cC(=N)[NH2] cC(=N)[NH2] 38: smi match: O=CN[OH] O=CN[OH] 38: smi match: NN NN +62: [09:20:25] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +62: [09:20:25] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 38: smi match: * * -70: *************************************** -70: *************************************** -70: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 38: smi match: *OP(=O)O* *OP(=O)O* -69: Using new chirality perception -69: Test -69: -69: rxnStereoMarkedCrossed.mrv -69: -69: Test -69: -69: 145323811.mol -69: -69: [12:00:55] unsupported number of radical electrons 5 -47: [12:00:55] Explicit valence for atom # 1 O, 3, is greater than permitted -47: [12:00:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -47: [12:00:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -47: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -16: ......... -16: ---------------------------------------------------------------------- -16: Ran 9 tests in 0.027s -16: -16: OK -74: [12:00:55] Finished: testSdf() -74: [12:00:55] ----------------------------------------- -74: -74: [12:00:55] -74: ----------------------------------------- 38: smi match: * * -47: [12:00:55] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. -47: [12:00:55] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom -47: [12:00:55] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom -47: [12:00:55] non-ring atom 0 marked aromatic +64: [09:20:25] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry + 48/235 Test #21: testPyGeometry ......................... Passed 1.58 sec +test 68 + Start 68: pyDepictor + +68: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/Wrap/testDepictor.py" +68: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap +68: Test timeout computed to be: 1500 38: smi match: * * 38: smi match: * * 38: smi match: *N=C(*)* *N=C(*)* @@ -17963,53 +17914,26 @@ 38: smi match: * * 38: smi match: O=CCl O=CCl 38: smi match: *** *** - 43/235 Test #77: testTplParser .......................... Passed 0.08 sec -test 85 - Start 85: molfileStereoCatchTest - -85: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest -85: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -85: Test timeout computed to be: 1500 38: smi match: *C=O *C=O 38: smi match: C[OH] C[OH] 38: smi match: C[OH] C[OH] 38: smi match: C[OH] C[OH] 38: smi match: C[OH] C[OH] 38: smi match: C[CH]=O C[CH]=O -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -47: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -36: [12:00:55] WARNING: not removing hydrogen atom with dummy atom neighbors 38: smi match: *=* *=* 38: smi match: *C *C 38: smi match: C#C C#C 38: smi match: *[CH]C=C *[CH]C=C 38: smi match: cCC(=O)[OH] cCC(=O)[OH] -74: [12:00:55] Finished: testSmi() -74: [12:00:55] ----------------------------------------- -74: -74: [12:00:55] -74: ----------------------------------------- - 44/235 Test #78: testMol2ToMol .......................... Passed 0.09 sec - 45/235 Test #80: testExtendedStereoParsing .............. Passed 0.07 sec -test 86 - Start 86: connectTheDotsTest - -86: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest -86: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -86: Test timeout computed to be: 1500 -test 87 - Start 87: v2MolSuppliers - -87: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers -87: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -87: Test timeout computed to be: 1500 -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -36: ------------------------------- -36: [12:00:55] Explicit valence for atom # 0 N, 4, is greater than permitted 38: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] 38: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] + 49/235 Test #62: smaTest1 ............................... Passed 0.34 sec +test 69 + Start 69: testMrvToMol + +69: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +69: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse +69: Test timeout computed to be: 1500 38: smi match: C=CC(=O)[OH] C=CC(=O)[OH] 38: smi match: N#CC(=O)[OH] N#CC(=O)[OH] 38: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O @@ -18023,30 +17947,337 @@ 38: smi match: *C(*)=O *C(*)=O 38: smi match: * * 38: smi match: *CC(=O)[OH] *CC(=O)[OH] +47: [09:20:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [09:20:25] Explicit valence for atom # 0 Al, 6, is greater than permitted +47: [09:20:25] Explicit valence for atom # 0 Al, 6, is greater than permitted +47: [09:20:25] Explicit valence for atom # 1 Si, 6, is greater than permitted +47: [09:20:25] Explicit valence for atom # 1 Si, 6, is greater than permitted +47: [09:20:25] Explicit valence for atom # 0 P, 6, is greater than permitted +47: [09:20:25] Explicit valence for atom # 0 P, 6, is greater than permitted +47: [09:20:25] Explicit valence for atom # 0 P, 7, is greater than permitted +47: [09:20:25] Explicit valence for atom # 0 P, 7, is greater than permitted +47: [09:20:25] Explicit valence for atom # 1 As, 6, is greater than permitted +47: [09:20:25] Explicit valence for atom # 1 As, 6, is greater than permitted +47: [09:20:25] Explicit valence for atom # 1 As, 7, is greater than permitted +47: [09:20:25] Explicit valence for atom # 1 As, 7, is greater than permitted +47: [09:20:25] Explicit valence for atom # 0 Sb, 6, is greater than permitted +47: [09:20:25] Explicit valence for atom # 0 Sb, 6, is greater than permitted +47: [09:20:25] Explicit valence for atom # 0 Sb, 7, is greater than permitted +47: [09:20:25] Explicit valence for atom # 0 Sb, 7, is greater than permitted +47: [09:20:25] Explicit valence for atom # 1 Bi, 6, is greater than permitted +47: [09:20:25] Explicit valence for atom # 1 Bi, 6, is greater than permitted +47: [09:20:25] Explicit valence for atom # 1 Bi, 8, is greater than permitted +47: [09:20:25] Explicit valence for atom # 1 Bi, 8, is greater than permitted +47: =============================================================================== +47: All tests passed (4464 assertions in 106 test cases) +47: +64: [09:20:25] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +64: [09:20:25] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry + 50/235 Test #47: graphmolTestsCatch ..................... Passed 0.79 sec 38: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O 38: smi match: *c *c 38: smi match: CN(C)c CN(C)c 38: smi match: c c -81: Randomness seeded to: 2661461502 -81: [12:00:55] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -81: [12:00:55] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -81: [12:00:55] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -81: [12:00:55] SGroup 1 is invalid and will be ignored -81: [12:00:55] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -81: [12:00:55] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -81: [12:00:55] SGroup 1 is invalid and will be ignored -81: [12:00:55] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -81: [12:00:55] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -81: [12:00:55] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -81: [12:00:55] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -81: [12:00:55] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -81: [12:00:55] SGroup 1 is invalid and will be ignored -81: [12:00:55] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -81: [12:00:55] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -81: [12:00:55] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -81: [12:00:55] SGroup 1 is invalid and will be ignored -70: [12:00:55] bond with order 0 found on line 7. This is not part of the MDL specification. -73: [12:00:55] +38: smi match: *c *c +38: smi match: *c *c +38: smi match: **:*cF **:*cF +38: smi match: cB([OH])[OH] cB([OH])[OH] +38: smi match: N~N~N N~N~N +38: smi match: *N=N* *N=N* +38: smi match: *CC[OH] *CC[OH] +test 70 + Start 70: fileParsersTest1 + +70: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +70: Test timeout computed to be: 1500 +38: smi match: *CC[OH] *CC[OH] +38: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] +38: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] +38: smi match: *CCC(=O)[OH] *CCC(=O)[OH] +38: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] +38: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O +38: smi match: *OC(*)=O *OC(*)=O +38: smi match: *C(=O)[OH] *C(=O)[OH] +38: smi match: O=C[OH] O=C[OH] +38: smi match: *OC(=O)O* *OC(=O)O* +38: smi match: * * +38: smi match: *OC(=O)Cl *OC(=O)Cl +38: smi match: *C#N *C#N +38: smi match: NCC(=O)NCC=O NCC(=O)NCC=O +38: smi match: SS SS +38: smi match: * * +64: [09:20:25] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +64: [09:20:25] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +38: smi match: *=* *=* +38: smi match: *=* *=* +38: smi match: *=* *=* +38: smi match: *=* *=* +38: smi match: C1CO1 C1CO1 +38: smi match: *OC(*)=O *OC(*)=O +38: smi match: * * +38: smi match: *O*[OH] *O*[OH] +38: smi match: COC(C)(C)O COC(C)(C)O +38: smi match: *[OH] *[OH] +38: smi match: ** ** +38: smi match: C=N[NH2] C=N[NH2] +38: smi match: C=NC=O C=NC=O +38: smi match: * * +38: smi match: C#NC C#NC +38: smi match: CN=C=O CN=C=O +38: smi match: CN=C=S CN=C=S +38: smi match: *OC(*)(*)O* *OC(*)(*)O* +38: smi match: *C(*)=O *C(*)=O +38: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C +38: smi match: *~*=O *~*=O +38: smi match: *~*=O *~*=O +38: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] + 51/235 Test #32: pyDistGeom ............................. Passed 1.47 sec +38: smi match: * * +38: smi match: *C#N *C#N +test 71 + Start 71: testAtropisomers + +71: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers +71: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +71: Test timeout computed to be: 1500 +38: smi match: *N(=O)~O *N(=O)~O +38: smi match: N N +38: smi match: OC(=O)C(O)=O OC(=O)C(O)=O +38: smi match: C=NO C=NO +38: smi match: O~O O~O +38: smi match: c[OH] c[OH] +38: smi match: O=P(~[OH])~O O=P(~[OH])~O +38: smi match: CO~P(=O)~O CO~P(=O)~O +38: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O +38: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O +38: smi match: O=P(~O)~O O=P(~O)~O +38: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O +38: smi match: C[NH2] C[NH2] +38: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 +38: smi match: * * +38: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 +38: smi match: CS(C)~O CS(C)~O +38: smi match: CS(C)(~O)~O CS(C)(~O)~O +38: smi match: CS(N)(~O)~O CS(N)(~O)~O +38: smi match: CS([OH])(~O)~O CS([OH])(~O)~O +38: smi match: COS(C)(~O)~O COS(C)(~O)~O +38: smi match: *S(C)(~O)~O *S(C)(~O)~O +38: smi match: CN(C)C CN(C)C +38: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 +38: smi match: *C(*)=S *C(*)=S +38: smi match: *OC(*)=S *OC(*)=S +38: smi match: * * +38: smi match: C[SH] C[SH] +38: smi match: c[SH] c[SH] +38: smi match: NC(N)=S NC(N)=S +38: smi match: * * +38: smi match: ***** ***** +38: smi match: NC(N)=O NC(N)=O +38: [09:20:26] done +38: [09:20:26] ------------------------------------- +38: [09:20:26] Testing sf.net issue 280. +63: [09:20:26] w block attempts to set wedging on bond 0 more than once. +63: [09:20:26] improperly formatted w block +59: --C1CCC2(CC1)CCCCC2CCC1CCCC1 +38: [09:20:26] done +38: [09:20:26] ------------------------------------- +38: [09:20:26] Testing sf.net issue 285. +38: [09:20:26] done +38: [09:20:26] done +38: [09:20:26] done +38: [09:20:26] done +38: [09:20:26] done +38: [09:20:26] done +38: [09:20:26] done +38: [09:20:26] ------------------------------------- +38: [09:20:26] Testing Github2441: Add RDProps interface to Conformers. +38: [09:20:26] done +38: [09:20:26] ------------------------------------- +38: [09:20:26] Testing Issue2510: Pickle Confs as double. +38: [09:20:26] done +38: [09:20:26] ------------------------------------- +38: [09:20:26] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +38: [09:20:26] done +38: [09:20:26] ------------------------------------- +38: [09:20:26] Testing loading pickled mols with conformers +63: [09:20:26] atom 3 is not associated with bond 1(1-2) in w block +38: [09:20:26] done +38: [09:20:26] ------------------------------------- +38: [09:20:26] Testing conformer reading/writing options +38: [09:20:26] done +38: [09:20:26] ------------------------------------- +38: [09:20:26] Testing property reading options +38: [09:20:26] done +38: [09:20:26] ------------------------------------- +38: [09:20:26] Testing property reading options +38: [09:20:26] done +38: [09:20:26] ------------------------------------- +38: [09:20:26] Testing boost::serialization integration +38: [09:20:26] done +38: [09:20:26] ------------------------------------- +38: [09:20:26] Testing github issue 6036 + 52/235 Test #38: graphmoltestPickler .................... Passed 1.25 sec +test 72 + Start 72: testSquiggleDoubleBonds + +72: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds +72: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +72: Test timeout computed to be: 1500 +30: ......[09:20:26] Molecule does not have explicit Hs. Consider calling AddHs() +64: [09:20:26] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +64: [09:20:26] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +71: [09:20:26] ---- Running with POSIX locale ----- +64: [09:20:26] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +64: =============================================================================== +64: All tests passed (308 assertions in 9 test cases) +64: + 53/235 Test #64: nontetrahedralCatch .................... Passed 0.46 sec +test 73 + Start 73: testMolSupplier + +73: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +73: Test timeout computed to be: 1500 +73: [09:20:26] +73: ----------------------------------------- +67: Randomness seeded to: 793474824 +67: =============================================================================== +67: All tests passed (580 assertions in 18 test cases) +67: +70: *************************************** +70: *************************************** +63: [09:20:26] +63: +63: **** +63: Range Error +63: idx +63: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +63: Failed Expression: 20 < 20 +63: ---------- +63: Stacktrace: +63: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +63: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +63: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +63: 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-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +63: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +63: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +63: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +63: 7# 0x000056248AB1B323 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 8# 0x000056248AB6C628 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 9# 0x000056248AB6D148 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 10# 0x000056248AB6D5C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 11# 0x000056248AB3EC03 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 12# 0x000056248AB3EF6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 13# 0x000056248AAD0C8E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 14# 0x00007F774562ED68 in /lib/x86_64-linux-gnu/libc.so.6 +63: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +63: 16# 0x000056248AAD0CD1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: ---------- +63: **** +63: + 54/235 Test #67: depictorCatch .......................... Passed 0.41 sec +test 74 + Start 74: testGeneralFileReader + +74: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +74: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +74: Test timeout computed to be: 1500 +59: smi: ClC1CCCCC1 +59: smi: ClC1CCCCC1 +59: smi: ClC1CCCCC1Br +59: smi: c1ccccc1 +59: smi: c1ccncc1 +59: smi: c1cc[nH]c1 +59: smi: c1cc[nH]c1 +59: smi: c1cc[pH]c1 +70: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +59: [09:20:26] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +71: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: Randomness seeded to: 811845045 +72: =============================================================================== +72: All tests passed (15 assertions in 3 test cases) +72: +59: [09:20:26] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. + 55/235 Test #72: testSquiggleDoubleBonds ................ Passed 0.17 sec +71: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 75 + Start 75: testMultithreadedMolSupplier + +75: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier +75: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +75: Test timeout computed to be: 1500 +74: [09:20:26] +74: ----------------------------------------- +74: [09:20:26] Finished: testDetermineFormat() +74: [09:20:26] ----------------------------------------- +74: +74: [09:20:26] +74: ----------------------------------------- +71: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +59: CbC(aC)aC +59: CaC(bC)aC +59: CbC(bC)aC +59: O.C +69: Using new chirality perception +69: Test +69: +69: rxnStereoMarkedCrossed.mrv +69: +69: Test +69: +69: 145323811.mol +69: +69: [09:20:26] unsupported number of radical electrons 5 +63: [09:20:26] +63: +63: **** +63: Range Error +63: idx +63: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +63: Failed Expression: 20 < 20 +63: ---------- +63: Stacktrace: +63: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +63: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +63: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +63: 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-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +63: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +63: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +63: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +63: 7# 0x000056248AB1B323 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 8# 0x000056248AB6C628 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 9# 0x000056248AB6D148 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 10# 0x000056248AB6D5C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 11# 0x000056248AB3EC03 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 12# 0x000056248AB3EF6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 13# 0x000056248AAD0C8E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 14# 0x00007F774562ED68 in /lib/x86_64-linux-gnu/libc.so.6 +63: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +63: 16# 0x000056248AAD0CD1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: ---------- +63: **** +63: +63: [09:20:26] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +63: [09:20:26] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +63: [09:20:26] SMARTS Parse Error: syntax error while parsing: C1C)foo +63: [09:20:26] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' +63: [09:20:26] SMILES Parse Error: extra close parentheses while parsing: C1C)foo +63: [09:20:26] SMILES Parse Error: check for mistakes around position 4: +63: [09:20:26] C1C)foo +63: [09:20:26] ~~~^ +63: [09:20:26] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' +71: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +59: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O +30: ... +30: ---------------------------------------------------------------------- +30: Ran 12 tests in 0.936s +30: +30: OK +71: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [09:20:26] 73: 73: **** 73: Invariant Violation @@ -18057,102 +18288,236 @@ 73: Stacktrace: 73: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 73: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -73: 2# 0x00007F09C9595422 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +73: 2# 0x00007F4347795422 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 73: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -73: 4# 0x0000555AD44083B4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 5# 0x0000555AD43DDADA in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 6# 0x0000555AD43E0E0B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 7# 0x00007F09C8A33D68 in /lib/x86_64-linux-gnu/libc.so.6 +73: 4# 0x000055FE3B32E3B4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 5# 0x000055FE3B303ADA in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 6# 0x000055FE3B306E0B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 7# 0x00007F4346C2ED68 in /lib/x86_64-linux-gnu/libc.so.6 73: 8# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -73: 9# 0x0000555AD43E29D1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 9# 0x000055FE3B3089D1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 73: ---------- 73: **** 73: -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -38: smi match: *c *c -36: [12:00:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -36: [12:00:55] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -81: [12:00:55] SGroup 3 referenced on line 40 not found. -81: [12:00:55] -81: -81: **** -81: Pre-condition Violation -81: no bonds -81: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp -81: Failed Expression: !d_bonds.empty() -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x00007F5414EDA71E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# 0x000055A5266BE769 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 16# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] SGroup 3 referenced on line 40 not found. -81: [12:00:55] -81: -81: **** -81: Pre-condition Violation -81: no bonds -81: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp -81: Failed Expression: !d_bonds.empty() -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x00007F5414EDA71E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# 0x000055A5266BE812 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 16# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] no bonds -81: [12:00:55] SGroup 1 is invalid and will be ignored -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -81: [12:00:55] SGroup line too short: 'M SBV 1 6' on line 42 -81: [12:00:55] SGroup 1 is invalid and will be ignored -38: smi match: *c *c -36: [12:00:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -81: [12:00:55] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -36: [12:00:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -36: [12:00:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -36: [12:00:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -36: [12:00:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -36: [12:00:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -36: -81: [12:00:55] SGroup 2 is invalid and will be ignored -82: Randomness seeded to: 1709522489 -82: =============================================================================== -82: All tests passed (95 assertions in 4 test cases) -82: +74: [09:20:26] Finished: testSdf() +74: [09:20:26] ----------------------------------------- +74: +74: [09:20:26] +74: ----------------------------------------- +59: [09:20:26] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +59: [09:20:26] SMILES Parse Error: check for mistakes around position 4: +59: [09:20:26] c%()ccccc%() +59: [09:20:26] ~~~^ +59: [09:20:26] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +59: [09:20:26] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +59: [09:20:26] SMILES Parse Error: check for mistakes around position 9: +59: [09:20:26] c%(100000)ccccc%(100000) +59: [09:20:26] ~~~~~~~~^ +59: [09:20:26] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +59: [09:20:26] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +75: [09:20:26] +75: ----------------------------------------- +63: =============================================================================== +63: All tests passed (1584 assertions in 68 test cases) +63: +59: [09:20:26] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +61: Randomness seeded to: 2607524990 +61: Test +61: +61: ShortAtropisomerNoCoords.cxsmi +61: +61: Test +61: +61: ShortAtropisomer.cxsmi +61: +61: Test +61: +61: ShortAtropisomerArom.cxsmi +61: +61: Test +61: +61: AtropManyChirals.cxsmi +61: +61: Test +61: +61: AtropManyChiralsEnhanced.cxsmi +61: +61: Test +61: +61: AtropManyChiralsEnhanced2.cxsmi +61: +61: Test +61: +61: AtropManyChiralsEnhanced3.cxsmi +61: +61: Test +61: +61: AtropManyChiralsEnhanced4.cxsmi +61: +61: Test +61: +61: BMS-986142_3d_chiral.cxsmi +61: +61: Test +61: +61: BMS-986142_3d.cxsmi +61: +61: Test +61: +61: BMS-986142_atrop1.cxsmi +61: +61: Test +61: +61: BMS-986142_atrop2.cxsmi +61: +61: Test +61: +61: BMS-986142_atrop3.cxsmi +61: +61: Test +61: +61: BMS-986142_atrop4.cxsmi +61: +61: Test +61: +61: BMS-986142_atrop5.cxsmi +61: +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored + 56/235 Test #63: smiTestCatch ........................... Passed 0.71 sec +test 76 + Start 76: testMolWriter + +76: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter +76: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +76: Test timeout computed to be: 1500 +74: [09:20:26] Finished: testSmi() +74: [09:20:26] ----------------------------------------- +74: +74: [09:20:26] +74: ----------------------------------------- +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [09:20:26] bond with order 0 found on line 7. This is not part of the MDL specification. +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +59: [09:20:26] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [09:20:26] SMILES Parse Error: check for mistakes around position 14: +59: [09:20:26] COc(c1)cccc1C# +59: [09:20:26] ~~~~~~~~~~~~~^ +59: [09:20:26] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [09:20:26] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [09:20:26] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [09:20:26] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [09:20:26] SMILES Parse Error: check for mistakes around position 14: +59: [09:20:26] COc(c1)cccc1C# +59: [09:20:26] ~~~~~~~~~~~~~^ +59: [09:20:26] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [09:20:26] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [09:20:26] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [09:20:26] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [09:20:26] SMILES Parse Error: check for mistakes around position 14: +59: [09:20:26] COc(c1)cccc1C# +59: [09:20:26] ~~~~~~~~~~~~~^ +59: [09:20:26] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [09:20:26] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [09:20:26] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: C=c1s/c2n(c1=O)CCCCCCC\N=2 +59: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 +59: [09:20:26] SMILES Parse Error: extra close parentheses while parsing: C) +59: [09:20:26] SMILES Parse Error: check for mistakes around position 2: +59: [09:20:26] C) +59: [09:20:26] ~^ +59: [09:20:26] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' + 57/235 Test #59: smiTest1 ............................... Passed 0.86 sec +test 77 + Start 77: testTplParser + +77: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser +77: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +77: Test timeout computed to be: 1500 +61: Test +61: +61: BMS-986142_atrop6.cxsmi +61: +61: Test +61: +61: BMS-986142_atropBad1.cxsmi +61: +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +70: [09:20:26] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +70: [09:20:26] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +61: Test +61: +61: BMS-986142_atropBad2.cxsmi +61: +61: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +70: [09:20:26] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +61: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +61: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +61: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 + 58/235 Test #30: pyForceFieldConstraints ................ Passed 1.96 sec +test 78 + Start 78: testMol2ToMol + +78: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol +78: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +78: Test timeout computed to be: 1500 +74: [09:20:26] Finished: testMae() +74: [09:20:26] ----------------------------------------- +74: +74: [09:20:26] +74: ----------------------------------------- +41: [09:20:26] sorting (hanoi sort) vectors +61: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +74: [09:20:26] Finished: testTdt() +74: [09:20:26] ----------------------------------------- +74: +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored + 59/235 Test #74: testGeneralFileReader .................. Passed 0.30 sec +70: generating smiles +test 79 + Start 79: testSequence + +79: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence +79: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +79: Test timeout computed to be: 1500 +70: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 +70: converting back +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored + 60/235 Test #77: testTplParser .......................... Passed 0.12 sec +test 80 + Start 80: testExtendedStereoParsing + +80: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing +80: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +80: Test timeout computed to be: 1500 +71: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +71: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: check isomorphism +71: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +73: [09:20:26] Finished: testMolSup() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- 79: Sequence: GREG 79: HELM: PEPTIDE1{G.R.E.G}$$$$ 79: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O @@ -18650,10 +19015,6 @@ 79: CONECT 163 164 164 170 79: CONECT 165 166 79: CONECT 166 167 -38: smi match: **:*cF **:*cF -38: smi match: cB([OH])[OH] cB([OH])[OH] -38: smi match: N~N~N N~N~N -38: smi match: *N=N* *N=N* 79: CONECT 167 168 168 169 79: CONECT 170 171 79: CONECT 171 172 174 @@ -18787,141 +19148,6 @@ 79: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C -81: [12:00:55] -81: -81: **** -81: Pre-condition Violation -81: bookmark not found -81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -81: Failed Expression: (lu != d_bondBookmarks.end()) -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x00007F5414EDA5AB in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x000055A5266BF3D2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 17# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] -81: -81: **** -81: Pre-condition Violation -81: bookmark not found -81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -81: Failed Expression: (lu != d_bondBookmarks.end()) -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x00007F5414EDA5AB in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x000055A5266BF47A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 17# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] bookmark not found -81: [12:00:55] -81: -81: **** -83: Randomness seeded to: 1116285066 -83: =============================================================================== -83: All tests passed (100 assertions in 2 test cases) -83: -38: smi match: *CC[OH] *CC[OH] -81: Pre-condition Violation -81: bond is not part of the SubstanceGroup -81: Violation occurred on line 200 in file ./Code/GraphMol/SubstanceGroup.cpp -81: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 4# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x00007F5414EDA71E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x000055A5266BF47A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 17# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] bond is not part of the SubstanceGroup -81: [12:00:55] SGroup 2 is invalid and will be ignored -81: [12:00:55] -81: -81: **** -81: Pre-condition Violation -81: bookmark not found -81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -81: Failed Expression: (lu != d_atomBookmarks.end()) -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x00007F5414EDA5AB in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x000055A5266BF7E9 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 17# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] -81: -81: **** -38: smi match: *CC[OH] *CC[OH] -38: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] -38: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] -38: smi match: *CCC(=O)[OH] *CCC(=O)[OH] 79: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 79: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O @@ -18990,45 +19216,10 @@ 79: ATOM 32 CG GLN A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 33 CD GLN A 4 0.000 0.000 0.000 1.00 0.00 C 79: ATOM 34 OE1 GLN A 4 0.000 0.000 0.000 1.00 0.00 O -81: Pre-condition Violation -81: bookmark not found -81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -81: Failed Expression: (lu != d_atomBookmarks.end()) -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x00007F5414EDA5AB in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x000055A5266BF891 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 17# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] bookmark not found -81: [12:00:55] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -81: [12:00:55] SGroup 2 is invalid and will be ignored - 46/235 Test #14: pyRealValueVect ........................ Passed 0.60 sec - 47/235 Test #82: testPropertyLists ...................... Passed 0.09 sec - 48/235 Test #83: XYZFileParserCatchTest ................. Passed 0.08 sec -81: [12:00:55] WARNING: final character of V3000 array is not ')' -81: [12:00:55] -81: -81: **** -38: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] -38: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O +73: [09:20:26] Finished: testRandMolSup() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- 79: ATOM 35 NE2 GLN A 4 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 36 N ASN A 5 0.000 0.000 0.000 1.00 0.00 N 79: ATOM 37 CA ASN A 5 0.000 0.000 0.000 1.00 0.00 C @@ -19116,299 +19307,6 @@ 79: 79: Sequence: LfPVXLfPVX 79: HELM: PEPTIDE1{L.[dF].P.V.[Orn].L.[dF].P.V.[Orn]}$PEPTIDE1,PEPTIDE1,10:R2-1:R1$$$ -test 88 - Start 88: v2FileParsersCatchTest - -88: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest -88: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -88: Test timeout computed to be: 1500 -test 89 - Start 89: multithreadedSupplierCatchTest - -89: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest -89: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -89: Test timeout computed to be: 1500 -test 90 - Start 90: testSubstructMatch - -90: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct -90: Test timeout computed to be: 1500 -81: Pre-condition Violation -81: bookmark not found -81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -81: Failed Expression: (lu != d_bondBookmarks.end()) -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x000055A5266BD0F3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 18# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] WARNING: final character of V3000 array is not ')' -81: [12:00:55] -81: -81: **** -81: Pre-condition Violation -81: bookmark not found -81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -81: Failed Expression: (lu != d_bondBookmarks.end()) -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x000055A5266BD18B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 18# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] bookmark not found -81: [12:00:55] SGroup 1 is invalid and will be ignored -81: [12:00:55] WARNING: final character of V3000 array is not ')' -81: [12:00:55] -81: -81: **** -81: Pre-condition Violation -81: bookmark not found -81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -81: Failed Expression: (lu != d_atomBookmarks.end()) -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x000055A5266BD4F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 18# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] WARNING: final character of V3000 array is not ')' -81: [12:00:55] -81: -81: **** -81: Pre-condition Violation -81: bookmark not found -81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -81: Failed Expression: (lu != d_atomBookmarks.end()) -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x000055A5266BD58C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 18# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] bookmark not found -81: [12:00:55] SGroup 1 is invalid and will be ignored -81: [12:00:55] -81: -81: **** -81: Pre-condition Violation -81: bookmark not found -81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -81: Failed Expression: (lu != d_bondBookmarks.end()) -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x000055A5266BD8F3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 18# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] -81: -81: **** -81: Pre-condition Violation -81: bookmark not found -81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -81: Failed Expression: (lu != d_bondBookmarks.end()) -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x000055A5266BD98C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 18# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] bookmark not found -81: [12:00:55] SGroup 2 is invalid and will be ignored -81: [12:00:55] -81: -81: **** -81: Pre-condition Violation -81: bookmark not found -81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -81: Failed Expression: (lu != d_atomBookmarks.end()) -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x000055A5266BDCF2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 18# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] -81: -81: **** -81: Pre-condition Violation -81: bookmark not found -81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -81: Failed Expression: (lu != d_atomBookmarks.end()) -81: ---------- -81: Stacktrace: -81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x000055A5266BDD8C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 -81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 18# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: ---------- -81: **** -81: -81: [12:00:55] bookmark not found -81: [12:00:55] SGroup 2 is invalid and will be ignored -38: smi match: *OC(*)=O *OC(*)=O -38: smi match: *C(=O)[OH] *C(=O)[OH] -38: smi match: O=C[OH] O=C[OH] -38: smi match: *OC(=O)O* *OC(=O)O* -38: smi match: * * -38: smi match: *OC(=O)Cl *OC(=O)Cl -38: smi match: *C#N *C#N -38: smi match: NCC(=O)NCC=O NCC(=O)NCC=O -38: smi match: SS SS -38: smi match: * * -38: smi match: *=* *=* -38: smi match: *=* *=* -38: smi match: *=* *=* -38: smi match: *=* *=* -38: smi match: C1CO1 C1CO1 -38: smi match: *OC(*)=O *OC(*)=O -38: smi match: * * -38: smi match: *O*[OH] *O*[OH] -38: smi match: COC(C)(C)O COC(C)(C)O 79: Smiles: CC(C)C[C@@H]1NC(=O)[C@H](CCCN)NC(=O)[C@H](C(C)C)NC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc2ccccc2)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CCCN)NC(=O)[C@H](C(C)C)NC(=O)[C@@H]2CCCN2C(=O)[C@@H](Cc2ccccc2)NC1=O 79: PDB: 79: ATOM 1 N LEU A 1 0.000 0.000 0.000 1.00 0.00 N @@ -19608,103 +19506,533 @@ 79: CONECT 27 28 28 29 79: END 79: -47: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 49/235 Test #13: pyDiscreteValueVect .................... Passed 0.62 sec - 50/235 Test #15: pySparseIntVect ........................ Passed 0.61 sec - 51/235 Test #79: testSequence ........................... Passed 0.14 sec -36: [12:00:55] WARNING: not removing hydrogen atom with dummy atom neighbors -test 91 - Start 91: substructTestCatch + 61/235 Test #79: testSequence ........................... Passed 0.07 sec +test 81 + Start 81: fileParsersCatchTest -91: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch -91: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct -91: Test timeout computed to be: 1500 -test 92 - Start 92: testGenericGroups +81: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +81: Test timeout computed to be: 1500 +71: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 62/235 Test #78: testMol2ToMol .......................... Passed 0.13 sec +test 82 + Start 82: testPropertyLists -92: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups -92: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups -92: Test timeout computed to be: 1500 -test 93 - Start 93: testReaction +82: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists +82: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +82: Test timeout computed to be: 1500 +81: Randomness seeded to: 2692653345 +81: [09:20:26] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +81: [09:20:26] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +81: [09:20:26] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +81: [09:20:26] SGroup 1 is invalid and will be ignored +81: [09:20:26] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +81: [09:20:26] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +81: [09:20:26] SGroup 1 is invalid and will be ignored +81: [09:20:26] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +81: [09:20:26] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +81: [09:20:26] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +81: [09:20:26] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +81: [09:20:26] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +81: [09:20:26] SGroup 1 is invalid and will be ignored +81: [09:20:26] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +81: [09:20:26] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +81: [09:20:26] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +81: [09:20:26] SGroup 1 is invalid and will be ignored +81: [09:20:26] SGroup 3 referenced on line 40 not found. +81: [09:20:26] +81: +81: **** +81: Pre-condition Violation +81: no bonds +81: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp +81: Failed Expression: !d_bonds.empty() +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x00007F445A0DA71E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# 0x00005637CF524769 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 16# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: +81: [09:20:26] SGroup 3 referenced on line 40 not found. +81: [09:20:26] +81: +81: **** +81: Pre-condition Violation +81: no bonds +81: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp +81: Failed Expression: !d_bonds.empty() +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x00007F445A0DA71E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# 0x00005637CF524812 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 16# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: +81: [09:20:26] no bonds +81: [09:20:26] SGroup 1 is invalid and will be ignored +81: [09:20:26] SGroup line too short: 'M SBV 1 6' on line 42 +81: [09:20:26] SGroup 1 is invalid and will be ignored +81: [09:20:26] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +81: [09:20:26] SGroup 2 is invalid and will be ignored +81: [09:20:26] +81: +81: **** +81: Pre-condition Violation +81: bookmark not found +81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +81: Failed Expression: (lu != d_bondBookmarks.end()) +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x00007F445A0DA5AB in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 8# 0x00005637CF5253D2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 17# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: +81: [09:20:26] +81: +81: **** +81: Pre-condition Violation +81: bookmark not found +81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +81: Failed Expression: (lu != d_bondBookmarks.end()) +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x00007F445A0DA5AB in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 8# 0x00005637CF52547A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 17# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: +81: [09:20:26] bookmark not found +81: [09:20:26] +81: +81: **** +81: Pre-condition Violation +81: bond is not part of the SubstanceGroup +81: Violation occurred on line 200 in file ./Code/GraphMol/SubstanceGroup.cpp +81: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 4# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x00007F445A0DA71E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 8# 0x00005637CF52547A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 17# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: +81: [09:20:26] bond is not part of the SubstanceGroup +81: [09:20:26] SGroup 2 is invalid and will be ignored +81: [09:20:26] +81: +81: **** +81: Pre-condition Violation +81: bookmark not found +81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +81: Failed Expression: (lu != d_atomBookmarks.end()) +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x00007F445A0DA5AB in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 8# 0x00005637CF5257E9 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 17# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: +81: [09:20:26] +81: +81: **** +81: Pre-condition Violation +81: bookmark not found +81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +81: Failed Expression: (lu != d_atomBookmarks.end()) +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x00007F445A0DA5AB in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 8# 0x00005637CF525891 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 17# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: +81: [09:20:26] bookmark not found +81: [09:20:26] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +81: [09:20:26] SGroup 2 is invalid and will be ignored +81: [09:20:26] WARNING: final character of V3000 array is not ')' +81: [09:20:26] +81: +81: **** +81: Pre-condition Violation +81: bookmark not found +81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +81: Failed Expression: (lu != d_bondBookmarks.end()) +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 9# 0x00005637CF5230F3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 18# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: +81: [09:20:26] WARNING: final character of V3000 array is not ')' +81: [09:20:26] +81: +81: **** +81: Pre-condition Violation +81: bookmark not found +81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +81: Failed Expression: (lu != d_bondBookmarks.end()) +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 9# 0x00005637CF52318B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 18# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: +81: [09:20:26] bookmark not found +81: [09:20:26] SGroup 1 is invalid and will be ignored +81: [09:20:26] WARNING: final character of V3000 array is not ')' +81: [09:20:26] +81: +81: **** +81: Pre-condition Violation +81: bookmark not found +81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +81: Failed Expression: (lu != d_atomBookmarks.end()) +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 9# 0x00005637CF5234F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 18# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: +81: [09:20:26] WARNING: final character of V3000 array is not ')' +81: [09:20:26] +81: +81: **** +81: Pre-condition Violation +81: bookmark not found +81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +81: Failed Expression: (lu != d_atomBookmarks.end()) +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 9# 0x00005637CF52358C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 18# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: +81: [09:20:26] bookmark not found +81: [09:20:26] SGroup 1 is invalid and will be ignored +81: [09:20:26] +81: +81: **** +81: Pre-condition Violation +81: bookmark not found +81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +81: Failed Expression: (lu != d_bondBookmarks.end()) +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 9# 0x00005637CF5238F3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 18# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: + 63/235 Test #80: testExtendedStereoParsing .............. Passed 0.12 sec +81: [09:20:26] +81: +81: **** +81: Pre-condition Violation +81: bookmark not found +81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +81: Failed Expression: (lu != d_bondBookmarks.end()) +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 9# 0x00005637CF52398C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 18# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: +81: [09:20:26] bookmark not found +81: [09:20:26] SGroup 2 is invalid and will be ignored +81: [09:20:26] +81: +81: **** +test 83 + Start 83: XYZFileParserCatchTest -93: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction -93: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -93: Test timeout computed to be: 1500 -85: Randomness seeded to: 2103664787 -85: [12:00:55] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -85: [12:00:55] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -85: [12:00:55] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -85: [12:00:55] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -85: =============================================================================== -85: All tests passed (142 assertions in 6 test cases) -85: -32: ...... -32: ---------------------------------------------------------------------- -32: Ran 6 tests in 0.005s -32: -32: OK -38: smi match: *[OH] *[OH] -38: smi match: ** ** -38: smi match: C=N[NH2] C=N[NH2] -38: smi match: C=NC=O C=NC=O -38: smi match: * * -38: smi match: C#NC C#NC -38: smi match: CN=C=O CN=C=O -38: smi match: CN=C=S CN=C=S -38: smi match: *OC(*)(*)O* *OC(*)(*)O* -38: smi match: *C(*)=O *C(*)=O -38: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C -38: smi match: *~*=O *~*=O -38: smi match: *~*=O *~*=O -38: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] -38: smi match: * * -38: smi match: *C#N *C#N -38: smi match: *N(=O)~O *N(=O)~O -38: smi match: N N -38: smi match: OC(=O)C(O)=O OC(=O)C(O)=O -38: smi match: C=NO C=NO -38: smi match: O~O O~O -38: smi match: c[OH] c[OH] -38: smi match: O=P(~[OH])~O O=P(~[OH])~O -38: smi match: CO~P(=O)~O CO~P(=O)~O -38: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O -38: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O -38: smi match: O=P(~O)~O O=P(~O)~O -38: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O -38: smi match: C[NH2] C[NH2] -38: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 -38: smi match: * * -38: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 -38: smi match: CS(C)~O CS(C)~O -38: smi match: CS(C)(~O)~O CS(C)(~O)~O -38: smi match: CS(N)(~O)~O CS(N)(~O)~O -38: smi match: CS([OH])(~O)~O CS([OH])(~O)~O -38: smi match: COS(C)(~O)~O COS(C)(~O)~O -38: smi match: *S(C)(~O)~O *S(C)(~O)~O -47: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -47: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -81: [12:00:55] Explicit valence for atom # 2 O, 3, is greater than permitted -81: [12:00:55] Explicit valence for atom # 1 O, 3, is greater than permitted -81: [12:00:55] Explicit valence for atom # 1 C, 5, is greater than permitted -81: [12:00:55] sanitize [12:00:55] UNK: [12:00:55] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -62: [12:00:55] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -62: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -62: [12:00:55] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -62: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -62: [12:00:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -62: [12:00:55] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -28: done -21: .................... -21: ---------------------------------------------------------------------- -21: Ran 20 tests in 0.132s -21: -21: OK -21: Testing Geometry wrapper -70: [12:00:55] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -70: [12:00:55] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -70: [12:00:55] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +83: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest +83: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +83: Test timeout computed to be: 1500 +81: Pre-condition Violation +81: bookmark not found +81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +81: Failed Expression: (lu != d_atomBookmarks.end()) +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 9# 0x00005637CF523CF2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 18# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: +81: [09:20:26] +81: +81: **** +81: Pre-condition Violation +81: bookmark not found +81: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +81: Failed Expression: (lu != d_atomBookmarks.end()) +81: ---------- +81: Stacktrace: +81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +81: 4# RDKit::SGroupParsing::ParseV3000ParseLabel(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_stringstream, std::allocator >&, std::vector, std::allocator >, std::allocator, std::allocator > > >&, unsigned int, RDKit::SubstanceGroup&, unsigned long, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 9# 0x00005637CF523D8C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +81: 18# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: ---------- +81: **** +81: +81: [09:20:26] bookmark not found +81: [09:20:26] SGroup 2 is invalid and will be ignored +81: [09:20:26] Explicit valence for atom # 2 O, 3, is greater than permitted +81: [09:20:26] Explicit valence for atom # 1 O, 3, is greater than permitted +81: [09:20:26] Explicit valence for atom # 1 C, 5, is greater than permitted 69: Test 69: 69: NewChiralTest.sdf @@ -19737,230 +20065,57 @@ 69: 69: ProblemShort.mol 69: -69: [12:00:55] For a MultipleSgroup expansion, the matching orphaned bond was not found +69: [09:20:26] For a MultipleSgroup expansion, the matching orphaned bond was not found 69: The multiple sgroup will be ignored -86: Randomness seeded to: 3645099646 -86: =============================================================================== -86: All tests passed (8 assertions in 1 test case) -86: -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored - 52/235 Test #16: pyFPB .................................. Passed 0.64 sec - 53/235 Test #25: pyAlignment ............................ Passed 0.58 sec - 54/235 Test #28: testUFFForceField ...................... Passed 0.55 sec - 55/235 Test #85: molfileStereoCatchTest ................. Passed 0.10 sec -38: smi match: CN(C)C CN(C)C -38: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 -38: smi match: *C(*)=S *C(*)=S -test 94 - Start 94: testReactionFingerprints - -94: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints -94: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -94: Test timeout computed to be: 1500 -test 95 - Start 95: testEnumeration - -95: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration -95: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -95: Test timeout computed to be: 1500 -test 96 - Start 96: rxnTestCatch - -96: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch -96: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -96: Test timeout computed to be: 1500 -test 97 - Start 97: pyChemReactions +71: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +81: [09:20:26] sanitize [09:20:26] UNK: [09:20:26] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +73: [09:20:26] Finished: testSmilesSup() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +73: [09:20:26] ------------------------------------------------------ +73: [09:20:26] SMILES Parse Error: syntax error while parsing: fail +73: [09:20:26] SMILES Parse Error: check for mistakes around position 1: +73: [09:20:26] fail +73: [09:20:26] ^ +73: [09:20:26] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +73: [09:20:26] ERROR: Smiles parse error on line 3 +73: [09:20:26] ERROR: Cannot create molecule from : 'fail' +73: [09:20:26] ------------------------------------------------------ +73: [09:20:26] ------------------------------------------------------ +73: [09:20:26] >>> This may result in an infinite loop. It should finish almost immediately: +73: [09:20:26] <<< done. +73: [09:20:26] Finished: testSmilesSupFromText() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +71: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +83: Randomness seeded to: 2443565311 +83: =============================================================================== +83: All tests passed (100 assertions in 2 test cases) +83: + 64/235 Test #83: XYZFileParserCatchTest ................. Passed 0.05 sec +71: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +test 84 + Start 84: cdxmlParserCatchTest -97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" -97: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -97: Test timeout computed to be: 1500 -38: smi match: *OC(*)=S *OC(*)=S -38: smi match: * * -38: smi match: C[SH] C[SH] -38: smi match: c[SH] c[SH] -38: smi match: NC(N)=S NC(N)=S -38: smi match: * * -38: smi match: ***** ***** -38: smi match: NC(N)=O NC(N)=O -38: [12:00:55] done -38: [12:00:55] ------------------------------------- -38: [12:00:55] Testing sf.net issue 280. -38: [12:00:55] done -38: [12:00:55] ------------------------------------- -38: [12:00:55] Testing sf.net issue 285. -38: [12:00:55] done -38: [12:00:55] done -38: [12:00:55] done -38: [12:00:55] done -38: [12:00:55] done -38: [12:00:55] done -38: [12:00:55] done -38: [12:00:55] ------------------------------------- -38: [12:00:55] Testing Github2441: Add RDProps interface to Conformers. -38: [12:00:55] done -38: [12:00:55] ------------------------------------- -38: [12:00:55] Testing Issue2510: Pickle Confs as double. -38: [12:00:55] done -38: [12:00:55] ------------------------------------- -38: [12:00:55] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -38: [12:00:55] done -38: [12:00:55] ------------------------------------- -38: [12:00:55] Testing loading pickled mols with conformers -38: [12:00:55] done -38: [12:00:55] ------------------------------------- -38: [12:00:55] Testing conformer reading/writing options -38: [12:00:55] done -38: [12:00:55] ------------------------------------- -38: [12:00:55] Testing property reading options -38: [12:00:55] done -38: [12:00:55] ------------------------------------- -38: [12:00:55] Testing property reading options -38: [12:00:55] done -38: [12:00:55] ------------------------------------- -38: [12:00:55] Testing boost::serialization integration -38: [12:00:55] done -38: [12:00:55] ------------------------------------- -38: [12:00:55] Testing github issue 6036 -61: Randomness seeded to: 1481195764 -61: Test -61: -61: ShortAtropisomerNoCoords.cxsmi -61: -61: Test -61: -61: ShortAtropisomer.cxsmi -61: -61: Test -61: -61: ShortAtropisomerArom.cxsmi -61: -61: Test -61: -61: AtropManyChirals.cxsmi -61: -61: Test -61: -61: AtropManyChiralsEnhanced.cxsmi -61: -61: Test -61: -61: AtropManyChiralsEnhanced2.cxsmi -61: -61: Test -61: -61: AtropManyChiralsEnhanced3.cxsmi -61: -61: Test -61: -61: AtropManyChiralsEnhanced4.cxsmi -61: -61: Test -61: -61: BMS-986142_3d_chiral.cxsmi -61: -61: Test -61: -61: BMS-986142_3d.cxsmi -61: -61: Test -61: -61: BMS-986142_atrop1.cxsmi -61: -61: Test -61: -61: BMS-986142_atrop2.cxsmi -61: -61: Test -61: -61: BMS-986142_atrop3.cxsmi -61: -61: Test -61: -61: BMS-986142_atrop4.cxsmi -61: -61: Test -61: -61: BMS-986142_atrop5.cxsmi -61: -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -90: ----------------- Test 1 -90: Done -90: -90: ----------------- Test 2 -90: Done -90: -90: ----------------- Test 3 -90: Done -90: -90: ----------------- Test 4 -90: Done -90: -90: ----------------- Test 5 -90: Done -90: -90: ----------------- Test 5 QueryRoot -90: Done -90: -90: ----------------- Test 6 (Issue71 related) -90: Done -90: -90: ----------------- Testing serial numbers on recursive queries -90: Done -90: -90: [12:00:55] ------------------------------------- -90: [12:00:55] Test multithreading -90: reading molecules -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.058s -2: -2: OK -47: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -47: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -87: Randomness seeded to: 3364482017 -87: =============================================================================== -87: All tests passed (12 assertions in 5 test cases) -87: -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -81: [12:00:55] skipping block at line 7: 'BEGIN ATOM' -84: Randomness seeded to: 3080758022 -84: [12:00:55] Invalid or missing fragment id from CDXML fragment, assigning new one... -84: [12:00:55] Explicit valence for atom # 3 N, 4, is greater than permitted -84: [12:00:55] CDXMLParser: failed sanitizing skipping fragment 32 -84: [12:00:55] Bad bond in CDXML skipping fragment 58... -84: [12:00:55] Invalid or missing fragment id from CDXML fragment, assigning new one... -84: [12:00:55] Bad bond in CDXML skipping fragment 58... - 56/235 Test #38: graphmoltestPickler .................... Passed 0.51 sec - 57/235 Test #62: smaTest1 ............................... Passed 0.33 sec - 58/235 Test #86: connectTheDotsTest ..................... Passed 0.12 sec - 59/235 Test #87: v2MolSuppliers ......................... Passed 0.11 sec -47: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -47: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +84: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest +84: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +84: Test timeout computed to be: 1500 +82: Randomness seeded to: 3739923997 +82: =============================================================================== +82: All tests passed (95 assertions in 4 test cases) +82: +73: [09:20:26] Finished: testSmilesWriter() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +81: [09:20:26] skipping block at line 7: 'BEGIN ATOM' 81: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL 81: END 81: -81: [12:00:55] + 65/235 Test #82: testPropertyLists ...................... Passed 0.09 sec +81: [09:20:26] 81: 81: **** 81: Pre-condition Violation @@ -19972,21 +20127,21 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x000055A5266F27F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x000055A5266ADD7D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 3# 0x00005637CF5587F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x00005637CF513D7D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 13# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:00:55] +81: [09:20:26] 81: 81: **** 81: Pre-condition Violation @@ -19998,21 +20153,21 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x000055A5266F27F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x000055A5266ADF58 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 3# 0x00005637CF5587F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x00005637CF513F58 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 13# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:00:55] +81: [09:20:26] 81: 81: **** 81: Pre-condition Violation @@ -20024,21 +20179,21 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x000055A5266F27F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x000055A5266AE391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 3# 0x00005637CF5587F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x00005637CF514391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 13# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:00:55] +81: [09:20:26] 81: 81: **** 81: Pre-condition Violation @@ -20050,51 +20205,29 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x000055A5266F27F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x000055A5266AE716 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 3# 0x00005637CF5587F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x00005637CF514716 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 13# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -70: generating smiles -test 98 - Start 98: pyChemReactionEnumerations - -98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" -98: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -98: Test timeout computed to be: 1500 -test 99 - Start 99: pyChemReactionSanitize - -99: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" -99: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -99: Test timeout computed to be: 1500 -test 100 - Start 100: testChemTransforms - -100: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms -100: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms -100: Test timeout computed to be: 1500 -test 101 - Start 101: chemTransformsTestCatch - -101: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms -101: Test timeout computed to be: 1500 -71: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -71: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -71: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -81: [12:00:55] +81: [09:20:26] 81: 81: **** +test 85 + Start 85: molfileStereoCatchTest + +85: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest +85: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +85: Test timeout computed to be: 1500 81: Pre-condition Violation 81: no stream 81: Violation occurred on line 577 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp @@ -20104,29 +20237,29 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x000055A5266F27F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x000055A5266AE993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 3# 0x00005637CF5587F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x00005637CF514993 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 13# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:00:55] Found a SCD/SED line with missing/empty SDT specification at line 21 -81: [12:00:55] Found a SCD/SED line with missing/empty SDT specification at line 20 -81: [12:00:55] BEGIN SGROUP line not found on line 14 -81: [12:00:55] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -81: [12:00:55] END SGROUP line not found on line 14 -81: [12:00:55] END SGROUP line not found on line 14 -81: [12:00:55] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -81: [12:00:55] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -81: [12:00:55] +81: [09:20:26] Found a SCD/SED line with missing/empty SDT specification at line 21 +81: [09:20:26] Found a SCD/SED line with missing/empty SDT specification at line 20 +81: [09:20:26] BEGIN SGROUP line not found on line 14 +81: [09:20:26] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +81: [09:20:26] END SGROUP line not found on line 14 +81: [09:20:26] END SGROUP line not found on line 14 +81: [09:20:26] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +81: [09:20:26] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +81: [09:20:26] 81: 81: **** 81: Range Error @@ -20141,117 +20274,38 @@ 81: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# 0x000055A5266F240F in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x000055A5266B3D93 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 6# 0x00005637CF55840F in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x00005637CF519D93 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 81: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 16# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:00:55] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -81: [12:00:55] Multiple ATTCHPT values for atom 2 on line 9 -70: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -70: converting back -63: [12:00:55] w block attempts to set wedging on bond 0 more than once. -63: [12:00:55] improperly formatted w block -63: [12:00:55] atom 3 is not associated with bond 1(1-2) in w block -88: Randomness seeded to: 3945481829 -88: =============================================================================== -88: All tests passed (6 assertions in 1 test case) -88: -61: Test -61: -61: BMS-986142_atrop6.cxsmi -61: -61: Test -61: -61: BMS-986142_atropBad1.cxsmi -61: -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -59: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -74: [12:00:55] Finished: testMae() -74: [12:00:55] ----------------------------------------- -74: -74: [12:00:55] -74: ----------------------------------------- -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -74: [12:00:55] Finished: testTdt() -74: [12:00:55] ----------------------------------------- -74: -94: [12:00:55] ------------------------------------- -94: [12:00:55] Test Reaction StructuralFingerprint -47: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 60/235 Test #74: testGeneralFileReader .................. Passed 0.25 sec - 61/235 Test #88: v2FileParsersCatchTest ................. Passed 0.10 sec -67: Randomness seeded to: 464400836 -67: =============================================================================== -67: All tests passed (580 assertions in 18 test cases) -67: -test 102 - Start 102: tautomerQueryTestCatch - -102: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch -102: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery -102: Test timeout computed to be: 1500 -test 103 - Start 103: pyTautomerQuery - -103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" -103: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap -103: Test timeout computed to be: 1500 -81: [12:00:55] Found a SCD/SED line with missing/empty SDT specification at line 12 -81: [12:00:55] SMARTS Parse Error: syntax error while parsing: [#6;R -81: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -81: [12:00:55] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -81: [12:00:55] Skipping empty SMARTS value for SMARTSQ. -81: [12:00:55] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -81: [12:00:55] Found a SCD/SED line with missing/empty SDT specification at line 12 -81: [12:00:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -81: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -61: Test -61: -61: BMS-986142_atropBad2.cxsmi -61: -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -70: check isomorphism -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 62/235 Test #32: pyDistGeom ............................. Passed 0.59 sec - 63/235 Test #67: depictorCatch .......................... Passed 0.31 sec -test 104 - Start 104: testSubgraphs1 - -104: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 -104: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -104: Test timeout computed to be: 1500 -test 105 - Start 105: testSubgraphs2 - -105: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 -105: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -105: Test timeout computed to be: 1500 -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -81: [12:00:55] WARNING: Skipping property bar because the value includes an illegal blank line -81: [12:00:55] WARNING: Skipping property baz because the value includes an illegal blank line -81: [12:00:55] WARNING: Skipping property bletch +81: [09:20:26] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +81: [09:20:26] Multiple ATTCHPT values for atom 2 on line 9 +81: [09:20:26] Found a SCD/SED line with missing/empty SDT specification at line 12 +81: [09:20:26] SMARTS Parse Error: syntax error while parsing: [#6;R +81: [09:20:26] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +81: [09:20:26] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +81: [09:20:26] Skipping empty SMARTS value for SMARTSQ. +81: [09:20:26] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +81: [09:20:26] Found a SCD/SED line with missing/empty SDT specification at line 12 +81: [09:20:26] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +81: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +81: [09:20:26] WARNING: Skipping property bar because the value includes an illegal blank line +81: [09:20:26] WARNING: Skipping property baz because the value includes an illegal blank line +81: [09:20:26] WARNING: Skipping property bletch 81: nope because the name includes a newline -81: [12:00:55] WARNING: Skipping property bletch +81: [09:20:26] WARNING: Skipping property bletch 81: nope2 because the name includes a newline -81: [12:00:55] +81: [09:20:26] 81: 81: **** 81: Post-condition Violation @@ -20263,26 +20317,26 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x00007F5414EC8391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x00007F5414ED39D2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x00007F5414ED4EAD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 3# 0x00007F445A0C8391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x00007F445A0D39D2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x00007F445A0D4EAD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x000055A52668546C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 9# 0x00005637CF4EB46C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 18# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:00:55] +81: [09:20:26] 81: 81: **** 81: Post-condition Violation @@ -20294,26 +20348,26 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x00007F5414EC8391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x00007F5414ED39D2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x00007F5414ED4EAD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 3# 0x00007F445A0C8391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x00007F445A0D39D2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x00007F445A0D4EAD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x000055A526684B4A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 9# 0x00005637CF4EAB4A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 18# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:00:55] +81: [09:20:26] 81: 81: **** 81: Post-condition Violation @@ -20325,26 +20379,26 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x00007F5414EC8391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x00007F5414ED1CFA in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x00007F5414ED207D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 3# 0x00007F445A0C8391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x00007F445A0D1CFA in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x00007F445A0D207D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x000055A526685414 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 9# 0x00005637CF4EB414 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 18# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:00:55] +81: [09:20:26] 81: 81: **** 81: Post-condition Violation @@ -20356,82 +20410,73 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x00007F5414EC8391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x00007F5414ED1CFA in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x00007F5414ED207D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 3# 0x00007F445A0C8391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x00007F445A0D1CFA in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x00007F445A0D207D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x000055A5266850B2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 9# 0x00005637CF4EB0B2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 18# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [12:00:55] atom 3 has a negative isotope value. line: 15 -94: [12:00:55] ------------------------------------- -94: [12:00:55] Test Reaction DifferenceFingerprint -30: ...[12:00:55] Molecule does not have explicit Hs. Consider calling AddHs() -93: smi: O=C1CNC(=O)CN1 -93: 1: O=C1CNC(=O)CN1 -93: 2: COOC - 64/235 Test #94: testReactionFingerprints ............... Passed 0.09 sec -90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -90: processing -90: launch :0 -90: launch :1 -test 106 - Start 106: subgraphsCatch - -106: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch -106: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -106: Test timeout computed to be: 1500 -90: launch :2 -90: launch :3 -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -104: ----------------------- -104: Subgraph retrieval -104: Finished -104: ----------------------- -104: testSubgraphs2a -73: [12:00:55] Finished: testMolSup() -73: [12:00:55] ----------------------------------------- +81: [09:20:26] atom 3 has a negative isotope value. line: 15 +61: Test +61: +61: JDQ443_3d.cxsmi +61: +61: Test +61: +61: JDQ443_atrop1.cxsmi +61: +61: Test +61: +61: JDQ443_atrop2.cxsmi +61: +61: Test +61: +61: JDQ443_atrop3.cxsmi +61: +61: Test +61: +61: JDQ443_atrop4.cxsmi +61: +61: Test +61: +61: JDQ443_atropBad1.cxsmi +61: +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +73: [09:20:26] Finished: testSDWriter() +73: [09:20:26] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -105: ----------------------- -105: Test1: pathToSubmol -93: [12:00:55] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [12:00:55] 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 -59: smi: ClC1CCCCC1 -59: smi: ClC1CCCCC1 -59: smi: ClC1CCCCC1Br -59: smi: c1ccccc1 -59: smi: c1ccncc1 -59: smi: c1cc[nH]c1 -59: smi: c1cc[nH]c1 -59: smi: c1cc[pH]c1 -41: [12:00:55] sorting (hanoi sort) vectors -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 4 -73: [12:00:55] Finished: testRandMolSup() -73: [12:00:55] ----------------------------------------- +73: [09:20:26] ----------------------------------------- +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +73: [09:20:26] Finished: testSDSupplierEnding() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +73: [09:20:26] Finished: testSuppliersEmptyFile() +73: [09:20:26] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -81: [12:00:55] +73: [09:20:26] ----------------------------------------- +73: [09:20:26] Finished: testCisTrans() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +81: [09:20:26] 81: 81: **** - 65/235 Test #21: testPyGeometry ......................... Passed 0.71 sec 81: Invariant Violation 81: bad prop value 81: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp @@ -20440,29 +20485,23 @@ 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# 0x00007F5414F95422 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 2# 0x00007F445A195422 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x000055A5266F27F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x000055A5266C743C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 4# 0x00005637CF5587F4 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x00005637CF52D43C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 81: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 14# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -test 107 - Start 107: filterCatalogTest - -107: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest -107: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog -107: Test timeout computed to be: 1500 -81: [12:00:55] +81: [09:20:26] 81: 81: **** 81: Pre-condition Violation @@ -20475,744 +20514,160 @@ 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x000055A5266C78C6 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x000055A526736328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x000055A526736E48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x000055A5267372C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x000055A5267089C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x000055A526708D2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x000055A52667BCAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x00007F5414433D68 in /lib/x86_64-linux-gnu/libc.so.6 +81: 4# 0x00005637CF52D8C6 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x00005637CF59C328 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x00005637CF59CE48 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x00005637CF59D2C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x00005637CF56E9C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x00005637CF56ED2C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x00005637CF4E1CAE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x00007F445962ED68 in /lib/x86_64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -81: 13# 0x000055A52667BCF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x00005637CF4E1CF1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -59: [12:00:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -59: [12:00:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -104: Finished -104: ----------------------- -104: testSubgraphs2 -100: 1 smi: CC -100: 1 smi: CC -100: 2 smi: CCO[C@H](N)P -100: 2 smi: CC -100: replaceSub smi1:CCP(CC)[C@@H](N)O -100: replaceSub smi1:CCNCC -100: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O -100: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O -84: [12:00:55] WARNING: not removing hydrogen atom without neighbors -84: [12:00:55] WARNING: not removing hydrogen atom without neighbors -84: [12:00:55] WARNING: not removing hydrogen atom without neighbors -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -105: Finished -105: ----------------------- -105: Test2: Atom Environments -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -59: CbC(aC)aC -59: CaC(bC)aC -93: [12:00:55] atom 0 in product 0 has multiple charge specifications. -59: CbC(bC)aC -105: Finished -105: ----------------------- -105: Test 3: Atom Environments (Extension) -93: mass: 15.0001 -59: O.C -105: Finished -105: ----------------------- -105: Testing github Issue103: stereochemistry and pathToSubmol -71: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -84: [12:00:55] WARNING: not removing hydrogen atom without neighbors -93: Oc1ccccn1 -93: Oc1ccc[nH]1 -84: [12:00:55] WARNING: not removing hydrogen atom without neighbors -59: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O -84: [12:00:55] WARNING: not removing hydrogen atom without neighbors -71: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -71: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -63: [12:00:55] -63: -63: **** -63: Range Error -63: idx -63: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -63: Failed Expression: 20 < 20 -63: ---------- -63: Stacktrace: -63: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -63: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -63: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -63: 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-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -63: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -63: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -63: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -63: 7# 0x000056372E391323 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 8# 0x000056372E3E2628 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 9# 0x000056372E3E3148 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 10# 0x000056372E3E35C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 11# 0x000056372E3B4C03 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 12# 0x000056372E3B4F6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 13# 0x000056372E346C8E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 14# 0x00007F8034033D68 in /lib/x86_64-linux-gnu/libc.so.6 -63: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -63: 16# 0x000056372E346CD1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: ---------- -63: **** -63: -59: [12:00:55] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -59: [12:00:55] SMILES Parse Error: check for mistakes around position 4: -59: [12:00:55] c%()ccccc%() -59: [12:00:55] ~~~^ -59: [12:00:55] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -59: [12:00:55] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -59: [12:00:55] SMILES Parse Error: check for mistakes around position 9: -59: [12:00:55] c%(100000)ccccc%(100000) -59: [12:00:55] ~~~~~~~~^ -59: [12:00:55] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -59: [12:00:55] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -59: [12:00:55] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -105: Finished -105: ----------------------- -105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) -105: Finished -84: [12:00:55] WARNING: not removing hydrogen atom without neighbors -84: [12:00:55] WARNING: not removing hydrogen atom without neighbors - 66/235 Test #2: pyCoordGen ............................. Passed 0.87 sec - 67/235 Test #105: testSubgraphs2 ......................... Passed 0.06 sec -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 108 - Start 108: pyFilterCatalog - -108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" -108: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap -108: Test timeout computed to be: 1500 -test 109 - Start 109: testFragCatalog - -109: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog -109: Test timeout computed to be: 1500 -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -106: Randomness seeded to: 2687164145 -106: --------- -106: =============================================================================== -106: All tests passed (11 assertions in 1 test case) -106: -84: [12:00:55] WARNING: not removing hydrogen atom without neighbors -84: [12:00:55] WARNING: not removing hydrogen atom without neighbors -84: [12:00:55] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. -59: [12:00:55] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [12:00:55] SMILES Parse Error: check for mistakes around position 14: -59: [12:00:55] COc(c1)cccc1C# -59: [12:00:55] ~~~~~~~~~~~~~^ -59: [12:00:55] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [12:00:55] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [12:00:55] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [12:00:55] SMILES Parse Error: check for mistakes around position 14: -59: [12:00:55] COc(c1)cccc1C# -59: [12:00:55] ~~~~~~~~~~~~~^ -59: [12:00:55] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [12:00:55] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [12:00:55] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [12:00:55] SMILES Parse Error: check for mistakes around position 14: -59: [12:00:55] COc(c1)cccc1C# -59: [12:00:55] ~~~~~~~~~~~~~^ -59: [12:00:55] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [12:00:55] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: C=c1s/c2n(c1=O)CCCCCCC\N=2 -59: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 - 68/235 Test #106: subgraphsCatch ......................... Passed 0.06 sec -test 110 - Start 110: pyFragCatalog - -110: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap/rough_test.py" -110: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap -110: Test timeout computed to be: 1500 -59: [12:00:55] SMILES Parse Error: extra close parentheses while parsing: C) -59: [12:00:55] SMILES Parse Error: check for mistakes around position 2: -59: [12:00:55] C) -59: [12:00:55] ~^ -59: [12:00:55] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' - 69/235 Test #59: smiTest1 ............................... Passed 0.47 sec -test 111 - Start 111: testDescriptors - -111: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors -111: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -111: Test timeout computed to be: 1500 -93: [12:00:55] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -93: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -93: [12:00:55] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [12:00:55] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -93: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -93: [12:00:55] SMARTS Parse Error: syntax error while parsing: [C:2]) -93: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -101: Randomness seeded to: 3199642940 -101: [12:00:55] Incomplete atom labelling, cannot make bond -101: [12:00:55] -101: -101: **** -101: Invariant Violation -101: molzip: bond info already exists for end atom with label:1 -101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -101: Failed Expression: !bond.b -101: ---------- -101: Stacktrace: -101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000555FB0FDA256 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000555FB102BFE8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000555FB102CB08 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000555FB102CF80 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000555FB0FFE783 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000555FB0FFEAEC in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000555FB0FCE63E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F1C0CC33D68 in /lib/x86_64-linux-gnu/libc.so.6 -101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x0000555FB0FCE681 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: ---------- -101: **** -101: -100: [12:00:55] SMARTS Parse Error: syntax error while parsing: bar -100: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -93: [12:00:55] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [12:00:55] SMILES Parse Error: check for mistakes around position 2: -93: [12:00:55] [Q:1][C:2][C:3](=[O:4])[O:5] -93: [12:00:55] ~^ -93: [12:00:55] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' -93: [12:00:55] reactant 2 has no mapped atoms. -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -93: [12:00:55] >> Atoms within one molecule have different RXN roles. -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -63: [12:00:55] -63: -63: **** -63: Range Error -63: idx -63: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -63: Failed Expression: 20 < 20 -63: ---------- -63: Stacktrace: -63: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -63: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -63: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -63: 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-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -63: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -63: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -63: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -63: 7# 0x000056372E391323 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 8# 0x000056372E3E2628 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 9# 0x000056372E3E3148 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 10# 0x000056372E3E35C0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 11# 0x000056372E3B4C03 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 12# 0x000056372E3B4F6C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 13# 0x000056372E346C8E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 14# 0x00007F8034033D68 in /lib/x86_64-linux-gnu/libc.so.6 -63: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -63: 16# 0x000056372E346CD1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: ---------- -93: [12:00:55] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -93: [12:00:55] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -93: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -93: [12:00:55] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [12:00:55] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -93: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -93: [12:00:55] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -93: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -63: **** -63: -63: [12:00:55] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -63: [12:00:55] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -63: [12:00:55] SMARTS Parse Error: syntax error while parsing: C1C)foo -63: [12:00:55] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' -63: [12:00:55] SMILES Parse Error: extra close parentheses while parsing: C1C)foo -63: [12:00:55] SMILES Parse Error: check for mistakes around position 4: -63: [12:00:55] C1C)foo -63: [12:00:55] ~~~^ -63: [12:00:55] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -84: [12:00:55] Incomplete atom labelling, cannot make bond -84: [12:00:55] Incomplete atom labelling, cannot make bond -93: [12:00:55] reactant 0 has no mapped atoms. -93: [12:00:55] reactant 1 has no mapped atoms. -93: [12:00:55] reactant 3 has no mapped atoms. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 4 found multiple times. -93: [12:00:55] product atom-mapping number 5 found multiple times. -93: [12:00:55] product atom-mapping number 6 found multiple times. -93: [12:00:55] product atom-mapping number 7 found multiple times. -93: [12:00:55] product atom-mapping number 8 found multiple times. -93: [12:00:55] product atom-mapping number 12 found multiple times. -93: [12:00:55] product atom-mapping number 9 found multiple times. -93: [12:00:55] product atom-mapping number 10 found multiple times. -93: [12:00:55] product atom-mapping number 11 found multiple times. -93: [12:00:55] reactant 0 has no mapped atoms. -93: [12:00:55] reactant 1 has no mapped atoms. -93: [12:00:55] reactant 3 has no mapped atoms. -93: [12:00:55] reactant atom-mapping number 19 found multiple times. -93: [12:00:55] reactant atom-mapping number 25 found multiple times. -93: [12:00:55] reactant atom-mapping number 20 found multiple times. -93: [12:00:55] reactant atom-mapping number 21 found multiple times. -93: [12:00:55] reactant atom-mapping number 22 found multiple times. -93: [12:00:55] reactant atom-mapping number 23 found multiple times. -93: [12:00:55] reactant atom-mapping number 24 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -71: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -71: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -63: =============================================================================== -63: All tests passed (1584 assertions in 68 test cases) -63: -93: [12:00:55] product atom-mapping number 5 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 4 found multiple times. -93: [12:00:55] product atom-mapping number 5 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -47: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 4 found multiple times. -93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [12:00:55] product atom-mapping number 5 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 4 found multiple times. -93: [12:00:55] product atom-mapping number 5 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 4 found multiple times. -93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -71: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -111: [12:00:55] ------------------------------------- -111: [12:00:55] Test Crippen parameter acquisition. -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 4 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 4 found multiple times. -93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 4 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 4 found multiple times. -93: F[C@](Cl)(Br)O[C@](F)(Cl)Br -93: [12:00:55] product atom-mapping number 4 found multiple times. -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 4 found multiple times. -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 4 found multiple times. -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 4 found multiple times. -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 4 -93: [12:00:55] product atom-mapping number 3 found multiple times. -93: [12:00:55] product atom-mapping number 2 found multiple times. -93: [12:00:55] product atom-mapping number 1 found multiple times. -93: [12:00:55] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 4 -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: [12:00:55] Explicit valence for atom # 0 Al, 6, is greater than permitted -47: [12:00:55] Explicit valence for atom # 0 Al, 6, is greater than permitted -47: [12:00:55] Explicit valence for atom # 1 Si, 6, is greater than permitted -47: [12:00:55] Explicit valence for atom # 1 Si, 6, is greater than permitted -47: [12:00:55] Explicit valence for atom # 0 P, 6, is greater than permitted -47: [12:00:55] Explicit valence for atom # 0 P, 6, is greater than permitted -47: [12:00:55] Explicit valence for atom # 0 P, 7, is greater than permitted -47: [12:00:55] Explicit valence for atom # 0 P, 7, is greater than permitted -47: [12:00:55] Explicit valence for atom # 1 As, 6, is greater than permitted -47: [12:00:55] Explicit valence for atom # 1 As, 6, is greater than permitted -47: [12:00:55] Explicit valence for atom # 1 As, 7, is greater than permitted -47: [12:00:55] Explicit valence for atom # 1 As, 7, is greater than permitted -47: [12:00:55] Explicit valence for atom # 0 Sb, 6, is greater than permitted -47: [12:00:55] Explicit valence for atom # 0 Sb, 6, is greater than permitted -47: [12:00:55] Explicit valence for atom # 0 Sb, 7, is greater than permitted -47: [12:00:55] Explicit valence for atom # 0 Sb, 7, is greater than permitted -47: [12:00:55] Explicit valence for atom # 1 Bi, 6, is greater than permitted -47: [12:00:55] Explicit valence for atom # 1 Bi, 6, is greater than permitted -47: [12:00:55] Explicit valence for atom # 1 Bi, 8, is greater than permitted -47: [12:00:55] Explicit valence for atom # 1 Bi, 8, is greater than permitted -47: =============================================================================== -47: All tests passed (4464 assertions in 106 test cases) -47: - 70/235 Test #63: smiTestCatch ........................... Passed 0.49 sec -111: [12:00:55] done -111: [12:00:55] ------------------------------------- -111: [12:00:55] Test Crippen calculation. -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 112 - Start 112: testAUTOCORR2D - -112: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D -112: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -112: Test timeout computed to be: 1500 -96: Randomness seeded to: 997944789 -96: [12:00:55] atom 0 in product 0 has multiple charge specifications. -93: [12:00:55] product atom-mapping number 6 not found in reactants. -93: [12:00:55] product atom-mapping number 7 not found in reactants. -93: [12:00:55] product atom-mapping number 8 not found in reactants. -93: [12:00:55] product atom-mapping number 7 not found in reactants. -93: [12:00:55] product atom-mapping number 8 not found in reactants. -93: [12:00:55] product atom-mapping number 9 not found in reactants. -93: [12:00:55] product atom-mapping number 10 not found in reactants. -93: [12:00:55] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 6 -93: [12:00:55] product atom-mapping number 7 not found in reactants. -93: [12:00:55] product atom-mapping number 8 not found in reactants. -93: [12:00:55] product atom-mapping number 9 not found in reactants. -93: [12:00:55] product atom-mapping number 10 not found in reactants. -93: [12:00:55] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 6 -101: [12:00:55] Incomplete atom labelling, cannot make bond -101: [12:00:55] -101: -101: **** -101: Invariant Violation -101: molzip: bond info already exists for end atom with label:1 -101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -101: Failed Expression: !bond.b -101: ---------- -101: Stacktrace: -101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000555FB0FDA256 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000555FB102BFE8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000555FB102CB08 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000555FB102CF80 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000555FB0FFE783 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000555FB0FFEAEC in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000555FB0FCE63E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F1C0CC33D68 in /lib/x86_64-linux-gnu/libc.so.6 -101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x0000555FB0FCE681 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: ---------- -101: **** -101: - 71/235 Test #47: graphmolTestsCatch ..................... Passed 0.62 sec -test 113 - Start 113: testATF - -113: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF -113: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -113: Test timeout computed to be: 1500 -96: [12:00:55] Found a SCD/SED line with missing/empty SDT specification at line 34 -96: [12:00:55] Found a SCD/SED line with missing/empty SDT specification at line 36 -96: [12:00:55] Found a SCD/SED line with missing/empty SDT specification at line 38 -96: [12:00:55] Found a SCD/SED line with missing/empty SDT specification at line 40 -96: [12:00:55] Found a SCD/SED line with missing/empty SDT specification at line 42 -96: [12:00:55] Found a SCD/SED line with missing/empty SDT specification at line 87 -96: [12:00:55] Found a SCD/SED line with missing/empty SDT specification at line 89 -96: [12:00:55] Found a SCD/SED line with missing/empty SDT specification at line 91 -96: [12:00:55] Found a SCD/SED line with missing/empty SDT specification at line 93 -96: [12:00:55] Found a SCD/SED line with missing/empty SDT specification at line 95 -109: 21 -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] -111: [12:00:55] done -111: [12:00:55] ------------------------------------- -111: [12:00:55] Test Issue262: problems with Crippen calculation from pickles. -111: [12:00:55] done -111: [12:00:55] ------------------------------------- -111: [12:00:55] Test AMW calculation. -111: [12:00:55] done -111: [12:00:55] ------------------------------------- -111: [12:00:55] Test Exact MW calculation. -111: [12:00:55] done -111: [12:00:55] ------------------------------------- -111: [12:00:55] Test Labute ASA descriptors. -61: Test -61: -61: JDQ443_3d.cxsmi -61: -61: Test -61: -61: JDQ443_atrop1.cxsmi -61: -61: Test -61: -61: JDQ443_atrop2.cxsmi -61: -61: Test -61: -61: JDQ443_atrop3.cxsmi -61: -61: Test -61: -61: JDQ443_atrop4.cxsmi -61: -61: Test -61: -61: JDQ443_atropBad1.cxsmi -61: -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -111: [12:00:55] done -111: [12:00:55] ------------------------------------- -111: [12:00:55] Test TPSA descriptors. -84: [12:00:55] Incomplete atom labelling, cannot make bond -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -96: [12:00:55] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -73: [12:00:55] Finished: testSmilesSup() -73: [12:00:55] ----------------------------------------- +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +73: [09:20:26] Finished: testStereoRound() +73: [09:20:26] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -73: [12:00:55] ------------------------------------------------------ -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -73: [12:00:55] SMILES Parse Error: syntax error while parsing: fail -73: [12:00:55] SMILES Parse Error: check for mistakes around position 1: -73: [12:00:55] fail -73: [12:00:55] ^ -73: [12:00:55] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -73: [12:00:55] ERROR: Smiles parse error on line 3 -81: [12:00:55] ERROR: molecules without atoms cannot be exported to Maestro files. -73: [12:00:55] ERROR: Cannot create molecule from : 'fail' -73: [12:00:55] ------------------------------------------------------ -73: [12:00:55] ------------------------------------------------------ -73: [12:00:55] >>> This may result in an infinite loop. It should finish almost immediately: -73: [12:00:55] <<< done. -73: [12:00:55] Finished: testSmilesSupFromText() -73: [12:00:55] ----------------------------------------- +73: [09:20:26] ----------------------------------------- +73: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [09:20:26] Finished: testIssue226() +73: [09:20:26] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -112: [12:00:55] ---------------------------- -112: start test autocorr2D -96: [12:00:55] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -81: [12:00:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -81: [12:00:55] ERROR: the mol cannot be kekulized, and will not be written to the output file. -81: [12:00:55] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. -104: Finished -81: [12:00:55] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[12:00:55] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -81: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -81: [12:00:55] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -81: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: ----------------------- -104: Path retrieval -104: Finished -104: ----------------------- -104: Path retrieval2 -104: Finished -104: ----------------------- -104: Unique Subgraph retrieval -104: Finished -104: ----------------------- -104: testUniqueSubgraphs2 -96: [12:00:55] SMARTS Parse Error: unclosed ring for input: 'CC1' -96: [12:00:55] SMILES Parse Error: unclosed ring for input: 'CC1' -96: [12:00:55] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [12:00:55] product atom-mapping number 2 not found in reactants. -73: [12:00:55] Finished: testSmilesWriter() -73: [12:00:55] ----------------------------------------- +73: [09:20:26] ----------------------------------------- +73: [09:20:26] Finished: testTDTSupplier1() +73: [09:20:26] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -101: [12:00:55] Incomplete atom labelling, cannot make bond -101: [12:00:55] -101: -101: **** -101: Invariant Violation -101: molzip: bond info already exists for end atom with label:1 -101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -101: Failed Expression: !bond.b -101: ---------- -101: Stacktrace: -101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000555FB0FDA256 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000555FB102BFE8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000555FB102CB08 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000555FB102CF80 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000555FB0FFE783 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000555FB0FFEAEC in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000555FB0FCE63E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F1C0CC33D68 in /lib/x86_64-linux-gnu/libc.so.6 -101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x0000555FB0FCE681 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: ---------- -101: **** -101: -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -84: [12:00:55] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -84: [12:00:55] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -84: [12:00:55] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -84: [12:00:55] Failed to parse XML fragment 5 node: b attribute: Order: 5 -84: [12:00:55] Invalid or missing fragment id from CDXML fragment, assigning new one... -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 72/235 Test #100: testChemTransforms ..................... Passed 0.23 sec -96: [12:00:55] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [12:00:55] product atom-mapping number 2 not found in reactants. -test 114 - Start 114: testBCUT - -114: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT -114: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -114: Test timeout computed to be: 1500 -96: [12:00:55] CX Extensions: Substance group hierarchy is not always preserved. -96: [12:00:55] CX Extensions: Substance group hierarchy is not always preserved. -90: done -90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -90: processing2 -90: launch2 :0 -90: launch2 :1 -90: launch2 :2 -90: launch2 :3 -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -84: =============================================================================== -84: All tests passed (263 assertions in 7 test cases) -84: - 73/235 Test #84: cdxmlParserCatchTest ................... Passed 0.41 sec -test 115 - Start 115: testEEM - -115: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM -115: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -115: Test timeout computed to be: 1500 -73: [12:00:55] Finished: testSDWriter() -73: [12:00:55] ----------------------------------------- +73: [09:20:26] ----------------------------------------- +73: [09:20:26] Finished: testTDTSupplier2() +73: [09:20:26] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -73: [12:00:55] Finished: testSDSupplierEnding() -73: [12:00:55] ----------------------------------------- +73: [09:20:26] ----------------------------------------- +73: [09:20:26] Finished: testTDTSupplier3() +73: [09:20:26] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -71: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 - 74/235 Test #113: testATF ................................ Passed 0.08 sec -test 116 - Start 116: testPBF +73: [09:20:26] ----------------------------------------- +73: [09:20:26] Finished: testSDSupplierFromText() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +73: [09:20:26] ERROR: Problems encountered parsing data fields +73: [09:20:26] ERROR: moving to the beginning of the next molecule +73: [09:20:26] ERROR: Problems encountered parsing data fields +73: [09:20:26] ERROR: moving to the beginning of the next molecule +73: [09:20:26] Spurious data before the first property will be ignored +73: [09:20:26] Property will be truncated after the first blank line +73: [09:20:26] Property will be truncated after the first blank line +73: [09:20:26] Property will be truncated after the first blank line +73: [09:20:26] Finished: testSDSupplierStrLax1() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +85: Randomness seeded to: 432449851 +85: [09:20:26] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +85: [09:20:26] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +85: [09:20:26] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +85: [09:20:26] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +73: [09:20:26] ERROR: Problems encountered parsing data fields +73: [09:20:26] ERROR: moving to the beginning of the next molecule +73: [09:20:26] Property will be truncated after the first blank line +73: [09:20:26] Finished: testSDSupplierStrLax2() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +73: [09:20:26] ERROR: Problems encountered parsing data fields +73: [09:20:26] ERROR: moving to the beginning of the next molecule +73: [09:20:26] ERROR: Problems encountered parsing data fields +73: [09:20:26] ERROR: moving to the beginning of the next molecule +73: [09:20:26] Spurious data before the first property will be ignored +73: [09:20:26] Property will be truncated after the first blank line +73: [09:20:26] Property will be truncated after the first blank line +73: [09:20:26] Property will be truncated after the first blank line +73: [09:20:26] Finished: testSDSupplierFromTextStrLax1() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +73: [09:20:26] ERROR: Problems encountered parsing data fields +73: [09:20:26] ERROR: moving to the beginning of the next molecule +73: [09:20:26] Property will be truncated after the first blank line +73: [09:20:26] Finished: testSDSupplierFromTextStrLax2() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +73: [09:20:26] Finished: testIssue265() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +73: [09:20:26] ERROR: End of data field name not found +73: [09:20:26] ERROR: moving to the beginning of the next molecule +85: =============================================================================== +85: All tests passed (142 assertions in 6 test cases) +85: + 66/235 Test #85: molfileStereoCatchTest ................. Passed 0.12 sec +73: [09:20:26] Explicit valence for atom # 0 F, 2, is greater than permitted +73: [09:20:26] ERROR: Could not sanitize molecule ending on line 16 +73: [09:20:26] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +test 86 + Start 86: connectTheDotsTest -116: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF -116: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -116: Test timeout computed to be: 1500 -73: [12:00:55] Finished: testSuppliersEmptyFile() -73: [12:00:55] ----------------------------------------- +86: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest +86: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +86: Test timeout computed to be: 1500 +73: [09:20:26] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +73: [09:20:26] ERROR: moving to the beginning of the next molecule +73: [09:20:26] ERROR: Bond line too short: 'M END' on line 18 +73: [09:20:26] ERROR: moving to the beginning of the next molecule +73: [09:20:26] Finished: testSDErrorHandling() +73: [09:20:26] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -73: [12:00:55] Finished: testCisTrans() -73: [12:00:55] ----------------------------------------- +73: [09:20:26] ----------------------------------------- +73: [09:20:26] Finished: testIssue381() +73: [09:20:26] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -90: done -90: preprocessing 3 -90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 -90: processing3 -90: launch3 :0 -90: launch3 :1 -90: launch3 :2 -90: launch3 :3 -93: [12:00:55] 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 -101: [12:00:55] Incomplete atom labelling, cannot make bond -101: [12:00:55] Incomplete atom labelling, cannot make bond -101: [12:00:55] Incomplete atom labelling, cannot make bond -101: [12:00:55] -101: -101: **** -101: Invariant Violation -101: molzip: bond info already exists for end atom with label:1 -101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -101: Failed Expression: !bond.b -101: ---------- -101: Stacktrace: -101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000555FB0FDA256 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000555FB102BFE8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000555FB102CB08 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000555FB102CF80 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000555FB0FFE783 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000555FB0FFEAEC in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000555FB0FCE63E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F1C0CC33D68 in /lib/x86_64-linux-gnu/libc.so.6 -101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x0000555FB0FCE681 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: ---------- -101: **** -101: -73: [12:00:55] Finished: testStereoRound() -73: [12:00:55] ----------------------------------------- +73: [09:20:26] ----------------------------------------- +73: [09:20:26] Finished: testSetStreamIndices() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +73: [09:20:26] Finished: testMixIterAndRandom() +73: [09:20:26] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- +73: [09:20:26] ----------------------------------------- +73: build: +73: [09:20:26] Finished: testRemoveHs() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +71: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +71: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +71: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +84: Randomness seeded to: 1151761420 +84: [09:20:26] Invalid or missing fragment id from CDXML fragment, assigning new one... +84: [09:20:26] Explicit valence for atom # 3 N, 4, is greater than permitted +84: [09:20:26] CDXMLParser: failed sanitizing skipping fragment 32 +84: [09:20:26] Bad bond in CDXML skipping fragment 58... +84: [09:20:26] Invalid or missing fragment id from CDXML fragment, assigning new one... +84: [09:20:26] Bad bond in CDXML skipping fragment 58... 61: Test 61: 61: RP-6306_atrop1.cxsmi @@ -21233,140 +20688,29 @@ 61: 61: RP-6306_atrop5.cxsmi 61: -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -73: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -73: [12:00:55] Finished: testIssue226() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -96: [12:00:55] reactant 0 has no mapped atoms. -96: [12:00:55] product 0 has no mapped atoms. -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -96: [12:00:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [12:00:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [12:00:55] Explicit valence for atom # 1 O, 5, is greater than permitted -73: [12:00:55] Finished: testTDTSupplier1() -73: [12:00:55] ----------------------------------------- +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [09:20:26] Finished: testGetItemText() +73: [09:20:26] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -114: [12:00:55] ------------------------------------- -114: [12:00:55] Basic BCUT tests. -95: 30000000 30000000 -73: [12:00:55] Finished: testTDTSupplier2() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -116: [12:00:55] ------------------------------------- -116: [12:00:55] Basic PBF tests. -73: [12:00:55] Finished: testTDTSupplier3() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -96: =============================================================================== -96: All tests passed (722 assertions in 30 test cases) -96: -73: [12:00:55] Finished: testSDSupplierFromText() -73: [12:00:55] ----------------------------------------- -73: -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -73: [12:00:55] ----------------------------------------- - 75/235 Test #96: rxnTestCatch ........................... Passed 0.32 sec -test 117 - Start 117: testRDFcustom - -117: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom -117: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -117: Test timeout computed to be: 1500 -73: [12:00:55] ERROR: Problems encountered parsing data fields -73: [12:00:55] ERROR: moving to the beginning of the next molecule -73: [12:00:55] ERROR: Problems encountered parsing data fields -73: [12:00:55] ERROR: moving to the beginning of the next molecule -73: [12:00:55] Spurious data before the first property will be ignored -73: [12:00:55] Property will be truncated after the first blank line -73: [12:00:55] Property will be truncated after the first blank line -73: [12:00:55] Property will be truncated after the first blank line -73: [12:00:55] Finished: testSDSupplierStrLax1() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -73: [12:00:55] ERROR: Problems encountered parsing data fields -73: [12:00:55] ERROR: moving to the beginning of the next molecule -73: [12:00:55] Property will be truncated after the first blank line -73: [12:00:55] Finished: testSDSupplierStrLax2() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -73: [12:00:55] ERROR: Problems encountered parsing data fields -73: [12:00:55] ERROR: moving to the beginning of the next molecule -73: [12:00:55] ERROR: Problems encountered parsing data fields -73: [12:00:55] ERROR: moving to the beginning of the next molecule -73: [12:00:55] Spurious data before the first property will be ignored -73: [12:00:55] Property will be truncated after the first blank line -73: [12:00:55] Property will be truncated after the first blank line -73: [12:00:55] Property will be truncated after the first blank line -73: [12:00:55] Finished: testSDSupplierFromTextStrLax1() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -73: [12:00:55] ERROR: Problems encountered parsing data fields -73: [12:00:55] ERROR: moving to the beginning of the next molecule -73: [12:00:55] Property will be truncated after the first blank line -73: [12:00:55] Finished: testSDSupplierFromTextStrLax2() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -73: [12:00:55] Finished: testIssue265() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -101: [12:00:55] Incomplete atom labelling, cannot make bond -101: [12:00:55] -101: -101: **** -101: Invariant Violation -101: molzip: bond info already exists for end atom with label:1 -101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -101: Failed Expression: !bond.b -101: ---------- -101: Stacktrace: -101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000555FB0FDA256 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000555FB102BFE8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000555FB102CB08 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000555FB102CF80 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000555FB0FFE783 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000555FB0FFEAEC in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000555FB0FCE63E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F1C0CC33D68 in /lib/x86_64-linux-gnu/libc.so.6 -101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# 0x0000555FB0FCE681 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: ---------- -101: **** -101: -73: [12:00:55] ERROR: End of data field name not found -73: [12:00:55] ERROR: moving to the beginning of the next molecule -73: [12:00:55] Explicit valence for atom # 0 F, 2, is greater than permitted -73: [12:00:55] ERROR: Could not sanitize molecule ending on line 16 -73: [12:00:55] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -73: [12:00:55] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -73: [12:00:55] ERROR: moving to the beginning of the next molecule -73: [12:00:55] ERROR: Bond line too short: 'M END' on line 18 -73: [12:00:55] ERROR: moving to the beginning of the next molecule -73: [12:00:55] Finished: testSDErrorHandling() -73: [12:00:55] ----------------------------------------- +73: [09:20:26] ----------------------------------------- +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +81: [09:20:26] ERROR: molecules without atoms cannot be exported to Maestro files. +81: [09:20:26] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +81: [09:20:26] ERROR: the mol cannot be kekulized, and will not be written to the output file. +81: [09:20:26] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. +73: [09:20:26] Finished: testForwardSDSupplier() +73: [09:20:26] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- +73: [09:20:26] ----------------------------------------- 61: Test 61: 61: RP-6306_atrop6.cxsmi @@ -21375,429 +20719,245 @@ 61: 61: RP-6306_atropBad1.cxsmi 61: -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -107: Warning: molecule failed filter -107: Warning: molecule failed filter: reason hzone_phenol_A(479) -107: v = { -107: 0,23}, -107: 1,22}, -107: 2,20}, -107: 3,19}, -107: 4,25}, -107: 5,24}, -107: 6,18}, -107: 7,17}, -107: 8,16}, -107: 9,21}, -107: } -107: match = { -107: 0,23}, -107: 1,22}, -107: 2,20}, -107: 3,19}, -107: 4,25}, -107: 5,24}, -107: 6,18}, -107: 7,17}, -107: 8,16}, -107: 9,21}, -107: } -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -107: Warning: molecule failed filter -101: [12:00:55] -101: -101: **** -101: Invariant Violation -101: molzip: zipped Bond already exists, perhaps labels are duplicated -101: Violation occurred on line 735 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -101: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) -101: ---------- -101: Stacktrace: -101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 5# 0x0000555FB0FCF43D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000555FB102BFE8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000555FB102CB08 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000555FB102CF80 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000555FB0FFE783 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000555FB0FFEAEC in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000555FB0FCE63E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 12# 0x00007F1C0CC33D68 in /lib/x86_64-linux-gnu/libc.so.6 -101: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -101: 14# 0x0000555FB0FCE681 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: ---------- -101: **** -101: -111: [12:00:55] done -111: [12:00:55] ------------------------------------- -111: [12:00:55] Test Lipinski parameters. -101: =============================================================================== -101: All tests passed (674 assertions in 9 test cases) -101: -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +86: Randomness seeded to: 1556928753 +86: =============================================================================== +86: All tests passed (8 assertions in 1 test case) +86: + 67/235 Test #86: connectTheDotsTest ..................... Passed 0.14 sec +73: [09:20:26] Finished: testMissingCRSDSupplier() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +test 87 + Start 87: v2MolSuppliers + +87: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers +87: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +87: Test timeout computed to be: 1500 +73: [09:20:26] Finished: testIssue3482695() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +36: [09:20:26] Maximum BFS search size exceeded. +36: This is likely due to a highly symmetric fused ring system. +81: [09:20:26] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[09:20:26] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +81: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +81: [09:20:26] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +81: [09:20:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [09:20:26] ERROR: Cannot convert 'foo' to unsigned int on line 557 +73: [09:20:26] ERROR: moving to the beginning of the next molecule +73: [09:20:26] Finished: testIssue3525673() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +61: [09:20:26] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +73: [09:20:26] Finished: testBlankLinesInProps() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- +84: [09:20:26] WARNING: not removing hydrogen atom without neighbors +84: [09:20:26] WARNING: not removing hydrogen atom without neighbors +73: [09:20:26] Finished: testSkipLines() +73: [09:20:26] ----------------------------------------- +73: +73: [09:20:26] ----------------------------------------- 61: Test 61: 61: RP-6306_atropBad2.cxsmi 61: -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -73: [12:00:55] Finished: testIssue381() -73: [12:00:55] ----------------------------------------- +61: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +61: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +73: [09:20:26] Finished: testGitHub23() +73: [09:20:26] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -114: [12:00:55] done -114: [12:00:55] ------------------------------------- -114: [12:00:55] Larger BCUT tests. -107: Warning: molecule failed filter: reason cyano_imine_B(17) -107: v = { -107: 0,11}, -107: 1,12}, -107: 2,13}, -107: 3,14}, -107: 4,15}, -107: 5,10}, -107: 6,9}, -107: 7,8}, -107: 8,7}, -107: 9,6}, -107: 10,5}, -107: 11,17}, -107: 12,16}, -107: } -107: match = { -107: 0,11}, -107: 1,12}, -107: 2,13}, -107: 3,14}, -107: 4,15}, -107: 5,10}, -107: 6,9}, -107: 7,8}, -107: 8,7}, -107: 9,6}, -107: 10,5}, -107: 11,17}, -107: 12,16}, -107: } -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 - 76/235 Test #101: chemTransformsTestCatch ................ Passed 0.32 sec -test 118 - Start 118: testRDF - -118: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF -118: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -118: Test timeout computed to be: 1500 -107: Warning: molecule failed filter -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -73: [12:00:55] Finished: testSetStreamIndices() -73: [12:00:55] ----------------------------------------- +73: [09:20:26] ----------------------------------------- +61: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +73: [09:20:26] Finished: testGitHub88() +73: [09:20:26] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -107: Warning: molecule failed filter: reason keto_keto_gamma(5) -107: v = { -107: 0,0}, -107: 1,1}, -107: 2,2}, -107: 3,4}, -107: 4,5}, -107: 5,6}, -107: 6,7}, -107: 7,8}, -107: 8,9}, -107: 9,14}, -107: 10,15}, -107: 11,16}, -107: } -107: match = { -107: 0,0}, -107: 1,1}, -107: 2,2}, -107: 3,4}, -107: 4,5}, -107: 5,6}, -107: 6,7}, -107: 7,8}, -107: 8,9}, -107: 9,14}, -107: 10,15}, -107: 11,16}, -107: } -73: [12:00:55] Finished: testMixIterAndRandom() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -93: [12:00:55] product atom-mapping number 17 not found in reactants. -93: [12:00:55] product atom-mapping number 18 not found in reactants. -93: [12:00:55] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 12 -115: =>start test EEM -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 0 -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: build: -73: [12:00:55] Finished: testRemoveHs() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: Randomness seeded to: 370005606 -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -73: [12:00:55] Finished: testGetItemText() -73: [12:00:55] ----------------------------------------- +73: [09:20:26] ----------------------------------------- +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +84: [09:20:26] WARNING: not removing hydrogen atom without neighbors +84: [09:20:26] WARNING: not removing hydrogen atom without neighbors +84: [09:20:26] WARNING: not removing hydrogen atom without neighbors +84: [09:20:26] WARNING: not removing hydrogen atom without neighbors +84: [09:20:26] WARNING: not removing hydrogen atom without neighbors +84: [09:20:26] WARNING: not removing hydrogen atom without neighbors +61: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +87: Randomness seeded to: 2152270747 +87: =============================================================================== +87: All tests passed (12 assertions in 5 test cases) +87: +61: [09:20:26] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [09:20:26] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored + 68/235 Test #87: v2MolSuppliers ......................... Passed 0.06 sec +test 88 + Start 88: v2FileParsersCatchTest + +88: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest +88: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +88: Test timeout computed to be: 1500 +84: [09:20:27] WARNING: not removing hydrogen atom without neighbors +84: [09:20:27] WARNING: not removing hydrogen atom without neighbors +84: [09:20:27] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +71: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +71: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +71: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +71: [09:20:27] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +73: [09:20:27] Finished: testGitHub2285() +73: [09:20:27] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -30: ......[12:00:55] Molecule does not have explicit Hs. Consider calling AddHs() -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -66: [12:00:55] Warning: stereochemistry around double bond may be incorrect in depiction. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -73: [12:00:55] Finished: testForwardSDSupplier() -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -73: [12:00:55] ----------------------------------------- +73: [09:20:27] ----------------------------------------- +73: [09:20:27] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +73: [09:20:27] ERROR: Smiles parse error on line 1 +73: [09:20:27] ERROR: Cannot create molecule from : 'c1ccccc' +73: [09:20:27] SMILES Parse Error: extra open parentheses while parsing: C(C +73: [09:20:27] SMILES Parse Error: check for mistakes around position 2: +73: [09:20:27] C(C +73: [09:20:27] ~^ +73: [09:20:27] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +73: [09:20:27] ERROR: Smiles parse error on line 3 +73: [09:20:27] ERROR: Cannot create molecule from : 'C(C' +73: [09:20:27] Explicit valence for atom # 1 C, 5, is greater than permitted +73: [09:20:27] ERROR: Could not sanitize molecule on line 5 +73: [09:20:27] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +73: [09:20:27] Explicit valence for atom # 1 F, 2, is greater than permitted +73: [09:20:27] ERROR: Could not sanitize molecule ending on line 21 +73: [09:20:27] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +73: [09:20:27] Explicit valence for atom # 1 F, 2, is greater than permitted +73: [09:20:27] ERROR: Could not sanitize molecule ending on line 21 +73: [09:20:27] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +73: [09:20:27] Explicit valence for atom # 1 F, 2, is greater than permitted +73: [09:20:27] ERROR: Could not sanitize molecule ending on line 21 +73: [09:20:27] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +73: [09:20:27] ERROR: Atom line too short: ' -9.6' on line 28 +73: [09:20:27] ERROR: moving to the beginning of the next molecule +73: [09:20:27] Explicit valence for atom # 1 F, 2, is greater than permitted +73: [09:20:27] ERROR: Could not sanitize molecule ending on line 21 +73: [09:20:27] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +73: [09:20:27] ERROR: Atom line too short: ' -9.6' on line 28 +73: [09:20:27] ERROR: moving to the beginning of the next molecule +73: [09:20:27] Finished: testGitHub2479() +73: [09:20:27] ----------------------------------------- 73: -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -73: [12:00:55] ----------------------------------------- -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -73: [12:00:55] Finished: testMissingCRSDSupplier() -73: [12:00:55] ----------------------------------------- +73: [09:20:27] ----------------------------------------- +73: [09:20:27] 73: -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -73: [12:00:55] ----------------------------------------- -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -73: [12:00:55] Finished: testIssue3482695() -73: [12:00:55] ----------------------------------------- +73: **** +73: Invariant Violation +73: bad chiral bond +73: Violation occurred on line 161 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +73: Failed Expression: bnd +73: ---------- +73: Stacktrace: +73: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +73: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +73: 2# 0x00007F4347795A1A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +73: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +73: 4# 0x000055FE3B3098CE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 5# 0x000055FE3B30875B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 6# 0x00007F4346C2ED68 in /lib/x86_64-linux-gnu/libc.so.6 +73: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +73: 8# 0x000055FE3B3089D1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: ---------- +73: **** 73: -73: [12:00:55] ----------------------------------------- -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: [12:00:55] ERROR: Cannot convert 'foo' to unsigned int on line 557 -73: [12:00:55] ERROR: moving to the beginning of the next molecule -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -73: [12:00:55] Finished: testIssue3525673() -73: [12:00:55] ----------------------------------------- +73: [09:20:27] Finished: testGitHub2881() +73: [09:20:27] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -73: [12:00:55] Finished: testBlankLinesInProps() -73: [12:00:55] ----------------------------------------- +73: [09:20:27] ----------------------------------------- +73: [09:20:27] Finished: testGitHub3517() +73: [09:20:27] ----------------------------------------- 73: -73: [12:00:55] ----------------------------------------- -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. + 69/235 Test #73: testMolSupplier ........................ Passed 0.97 sec +71: [09:20:27] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +test 89 + Start 89: multithreadedSupplierCatchTest + +89: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest +89: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +89: Test timeout computed to be: 1500 +71: [09:20:27] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +71: [09:20:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +84: [09:20:27] Incomplete atom labelling, cannot make bond +71: [09:20:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [09:20:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +84: [09:20:27] Incomplete atom labelling, cannot make bond +76: [09:20:27] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +88: Randomness seeded to: 3537390039 +88: =============================================================================== +88: All tests passed (6 assertions in 1 test case) +88: +66: [09:20:27] Warning: stereochemistry around double bond may be incorrect in depiction. + 70/235 Test #88: v2FileParsersCatchTest ................. Passed 0.12 sec +test 90 + Start 90: testSubstructMatch + +90: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct +90: Test timeout computed to be: 1500 +76: 0.40201265 0.40201265 +76: -0.13299436 -0.13299436 +76: 1.00000017 1.00000017 +76: 0.8762226 0.8762226 +76: 0.9973909 0.9973909 +76: 1.00000003 1.00000003 +76: 0.36613799 0.36613799 +76: 2.1107185 2.1107185 +76: 0.99999982 0.99999982 +76: 2.48696157 2.48696157 +76: 1.00479935 1.00479935 +76: 0.99999999 0.99999999 +76: 3.03311841 3.03311841 +76: 2.23739955 2.23739955 +76: 1.0000001 1.0000001 +76: 3.00772337 3.00772337 +76: 0.37399294 0.37399294 +76: 2.07713325 2.07713325 +76: 3.0077234 3.0077234 +76: 0.37399312 0.37399312 +76: -0.07713336 -0.07713336 +84: [09:20:27] Incomplete atom labelling, cannot make bond +76: [09:20:27] bond with order 0 found on line 11. This is not part of the MDL specification. +76: [09:20:27] bond with order 0 found on line 16. This is not part of the MDL specification. +90: ----------------- Test 1 +90: Done +90: +90: ----------------- Test 2 +90: Done +90: +90: ----------------- Test 3 +90: Done +90: +90: ----------------- Test 4 +90: Done +90: +90: ----------------- Test 5 +90: Done +90: +90: ----------------- Test 5 QueryRoot +90: Done +90: +90: ----------------- Test 6 (Issue71 related) +90: Done +90: +90: ----------------- Testing serial numbers on recursive queries +90: Done +90: +90: [09:20:27] ------------------------------------- +90: [09:20:27] Test multithreading +90: reading molecules +71: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +71: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +71: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 61: Test 61: 61: RP-6306_3d.cxsmi @@ -21822,99 +20982,356 @@ 61: 61: Sotorasib_atrop5.cxsmi 61: -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [12:00:55] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -73: [12:00:55] Finished: testSkipLines() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -73: [12:00:55] Finished: testGitHub23() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -73: [12:00:55] Finished: testGitHub88() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -90: done -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: [12:00:55] done -90: [12:00:55] ------------------------------------- -90: [12:00:55] Test GitHub issue 15 -90: [12:00:55] done -90: [12:00:55] ------------------------------------- -90: [12:00:55] Test GitHub issue 409 -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: [12:00:55] done -90: [12:00:55] ------------------------------------- -90: [12:00:55] Test chiral matching -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -90: [12:00:55] done -90: [12:00:55] ------------------------------------- -90: [12:00:55] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -90: [12:00:55] done -90: [12:00:55] ------------------------------------- -90: [12:00:55] Test dative-bond matching -90: [12:00:55] done -90: [12:00:55] ------------------------------------- -90: [12:00:55] Test cis/trans matching -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [12:00:55] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: [12:00:55] done -90: [12:00:55] ------------------------------------- -90: [12:00:55] Test cis/trans matching part 2 -90: [12:00:55] done -90: [12:00:55] ------------------------------------- -90: [12:00:55] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -90: [12:00:55] done +61: [09:20:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [09:20:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [09:20:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [09:20:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [09:20:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [09:20:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +84: [09:20:27] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +61: [09:20:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [09:20:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +84: [09:20:27] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +61: [09:20:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [09:20:27] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +71: [09:20:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [09:20:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +84: [09:20:27] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +84: [09:20:27] Failed to parse XML fragment 5 node: b attribute: Order: 5 +84: [09:20:27] Invalid or missing fragment id from CDXML fragment, assigning new one... 61: Test 61: 61: Sotorasib_atropBad1.cxsmi 61: -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -90: [12:00:55] ------------------------------------- -90: [12:00:55] Testing matching E/Z against Cis/Trans stereo bonds -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -76: [12:00:55] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -73: [12:00:55] Finished: testGitHub2285() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -73: [12:00:55] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -73: [12:00:55] ERROR: Smiles parse error on line 1 -73: [12:00:55] ERROR: Cannot create molecule from : 'c1ccccc' -73: [12:00:55] SMILES Parse Error: extra open parentheses while parsing: C(C -73: [12:00:55] SMILES Parse Error: check for mistakes around position 2: -73: [12:00:55] C(C -73: [12:00:55] ~^ -73: [12:00:55] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -73: [12:00:55] ERROR: Smiles parse error on line 3 -73: [12:00:55] ERROR: Cannot create molecule from : 'C(C' -73: [12:00:55] Explicit valence for atom # 1 C, 5, is greater than permitted -73: [12:00:55] ERROR: Could not sanitize molecule on line 5 -73: [12:00:55] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -73: [12:00:55] Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:00:55] ERROR: Could not sanitize molecule ending on line 21 -73: [12:00:55] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -90: [12:00:55] +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 + 71/235 Test #76: testMolWriter .......................... Passed 0.96 sec +71: [09:20:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 91 + Start 91: substructTestCatch + +91: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch +91: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct +91: Test timeout computed to be: 1500 +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +84: =============================================================================== +84: All tests passed (263 assertions in 7 test cases) +84: + 72/235 Test #84: cdxmlParserCatchTest ................... Passed 0.62 sec +test 92 + Start 92: testGenericGroups + +92: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups +92: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups +92: Test timeout computed to be: 1500 +61: Test +61: +61: Sotorasib_atropBad2.cxsmi +61: +61: [09:20:27] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +61: [09:20:27] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +61: [09:20:27] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +61: [09:20:27] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +90: processing +90: launch :0 +90: launch :1 +90: launch :2 +90: launch :3 +61: [09:20:27] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +71: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +71: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +71: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 + 73/235 Test #66: testDepictor ........................... Passed 1.85 sec +test 93 + Start 93: testReaction + +93: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction +93: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +93: Test timeout computed to be: 1500 +61: Test +61: +61: Sotorasib_3d.cxsmi +61: +61: Test +61: +61: ZM374979_atrop1.cxsmi +61: +61: Test +61: +61: ZM374979_atrop2.cxsmi +61: +61: Test +61: +61: ZM374979_atrop3.cxsmi +61: +61: Test +61: +61: ZM374979_atrop4.cxsmi +61: +61: Test +61: +61: ZM374979_atropBad1.cxsmi +61: +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +90: done +90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +90: processing2 +90: launch2 :0 +90: launch2 :1 +90: launch2 :2 +90: launch2 :3 +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +90: done +90: preprocessing 3 +90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 +90: processing3 +90: launch3 :0 +90: launch3 :1 +90: launch3 :2 +90: launch3 :3 +68: ..............[09:20:27] SMILES Parse Error: syntax error while parsing: invalidsmiles +68: [09:20:27] SMILES Parse Error: check for mistakes around position 1: +68: [09:20:27] invalidsmiles +68: [09:20:27] ^ +68: [09:20:27] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' +93: smi: O=C1CNC(=O)CN1 +93: 1: O=C1CNC(=O)CN1 +93: 2: COOC +93: [09:20:27] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [09:20:27] 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: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 4 +93: [09:20:27] atom 0 in product 0 has multiple charge specifications. +93: mass: 15.0001 +93: Oc1ccccn1 +93: Oc1ccc[nH]1 +93: [09:20:27] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +93: [09:20:27] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +93: [09:20:27] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [09:20:27] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [09:20:27] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +93: [09:20:27] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +93: [09:20:27] SMARTS Parse Error: syntax error while parsing: [C:2]) +93: [09:20:27] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +93: [09:20:27] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [09:20:27] SMILES Parse Error: check for mistakes around position 2: +93: [09:20:27] [Q:1][C:2][C:3](=[O:4])[O:5] +93: [09:20:27] ~^ +93: [09:20:27] 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]' +68: ..... +68: ---------------------------------------------------------------------- +68: Ran 19 tests in 0.823s +68: +68: OK +61: Test +61: +61: Mrtx1719_3d.cxsmi +61: +61: Test +61: +61: Mrtx1719_atrop1.cxsmi +61: +61: Test +61: +61: Mrtx1719_atrop2.cxsmi +61: +61: Test +61: +61: Mrtx1719_atrop3.cxsmi +61: +61: Test +61: +61: Mrtx1719_atrop4.cxsmi +61: +61: Test +61: +61: Mrtx1719_atropBad1.cxsmi +61: +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +93: [09:20:27] reactant 2 has no mapped atoms. +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +93: [09:20:27] >> Atoms within one molecule have different RXN roles. +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +93: [09:20:27] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +93: [09:20:27] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +93: [09:20:27] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +93: [09:20:27] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [09:20:27] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [09:20:27] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +93: [09:20:27] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +93: [09:20:27] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +93: [09:20:27] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +93: [09:20:27] reactant 0 has no mapped atoms. +93: [09:20:27] reactant 1 has no mapped atoms. +93: [09:20:27] reactant 3 has no mapped atoms. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 4 found multiple times. +93: [09:20:27] product atom-mapping number 5 found multiple times. +93: [09:20:27] product atom-mapping number 6 found multiple times. +93: [09:20:27] product atom-mapping number 7 found multiple times. +93: [09:20:27] product atom-mapping number 8 found multiple times. +93: [09:20:27] product atom-mapping number 12 found multiple times. +93: [09:20:27] product atom-mapping number 9 found multiple times. +93: [09:20:27] product atom-mapping number 10 found multiple times. +93: [09:20:27] product atom-mapping number 11 found multiple times. +93: [09:20:27] reactant 0 has no mapped atoms. +93: [09:20:27] reactant 1 has no mapped atoms. +93: [09:20:27] reactant 3 has no mapped atoms. +93: [09:20:27] reactant atom-mapping number 19 found multiple times. +93: [09:20:27] reactant atom-mapping number 25 found multiple times. +93: [09:20:27] reactant atom-mapping number 20 found multiple times. +93: [09:20:27] reactant atom-mapping number 21 found multiple times. +93: [09:20:27] reactant atom-mapping number 22 found multiple times. +93: [09:20:27] reactant atom-mapping number 23 found multiple times. +93: [09:20:27] reactant atom-mapping number 24 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +61: [09:20:27] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [09:20:27] product atom-mapping number 5 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 4 found multiple times. +93: [09:20:27] product atom-mapping number 5 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 4 found multiple times. +93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [09:20:27] product atom-mapping number 5 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 4 found multiple times. +93: [09:20:27] product atom-mapping number 5 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 4 found multiple times. +90: done +90: [09:20:27] done +90: [09:20:27] ------------------------------------- +90: [09:20:27] Test GitHub issue 15 +90: [09:20:27] done +90: [09:20:27] ------------------------------------- +90: [09:20:27] Test GitHub issue 409 +90: [09:20:27] done +90: [09:20:27] ------------------------------------- +90: [09:20:27] Test chiral matching +93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 4 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 4 found multiple times. +93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 4 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 4 found multiple times. +93: F[C@](Cl)(Br)O[C@](F)(Cl)Br +93: [09:20:27] product atom-mapping number 4 found multiple times. +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 4 found multiple times. +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 4 found multiple times. +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 4 found multiple times. +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 4 +93: [09:20:27] product atom-mapping number 3 found multiple times. +93: [09:20:27] product atom-mapping number 2 found multiple times. +93: [09:20:27] product atom-mapping number 1 found multiple times. +93: [09:20:27] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 4 +93: [09:20:27] product atom-mapping number 6 not found in reactants. +93: [09:20:27] product atom-mapping number 7 not found in reactants. +93: [09:20:27] product atom-mapping number 8 not found in reactants. +93: [09:20:27] product atom-mapping number 7 not found in reactants. +93: [09:20:27] product atom-mapping number 8 not found in reactants. +93: [09:20:27] product atom-mapping number 9 not found in reactants. +93: [09:20:27] product atom-mapping number 10 not found in reactants. +93: [09:20:27] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 6 +90: [09:20:27] done +90: [09:20:27] ------------------------------------- +90: [09:20:27] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +90: [09:20:27] done +90: [09:20:27] ------------------------------------- +90: [09:20:27] Test dative-bond matching +90: [09:20:27] done +90: [09:20:27] ------------------------------------- +90: [09:20:27] Test cis/trans matching +90: [09:20:27] done +90: [09:20:27] ------------------------------------- +90: [09:20:27] Test cis/trans matching part 2 +90: [09:20:27] done +90: [09:20:27] ------------------------------------- +90: [09:20:27] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +90: [09:20:27] done +93: [09:20:27] product atom-mapping number 7 not found in reactants. +93: [09:20:27] product atom-mapping number 8 not found in reactants. +93: [09:20:27] product atom-mapping number 9 not found in reactants. +93: [09:20:27] product atom-mapping number 10 not found in reactants. +93: [09:20:27] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 6 +90: [09:20:27] ------------------------------------- +90: [09:20:27] Testing matching E/Z against Cis/Trans stereo bonds + 74/235 Test #68: pyDepictor ............................. Passed 2.08 sec +test 94 + Start 94: testReactionFingerprints + +94: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints +94: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +94: Test timeout computed to be: 1500 +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] +90: [09:20:27] 90: 90: **** 90: Pre-condition Violation @@ -21927,15 +21344,15 @@ 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x00005647F734C42D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x00005647F733CC41 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x00007F10D9033D68 in /lib/x86_64-linux-gnu/libc.so.6 +90: 4# 0x00005631A311D42D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x00005631A310DC41 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x00007F87B242ED68 in /lib/x86_64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -90: 8# 0x00005647F733CD81 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 8# 0x00005631A310DD81 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: -90: [12:00:55] +90: [09:20:27] 90: 90: **** 90: Pre-condition Violation @@ -21948,182 +21365,1509 @@ 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 3# RDKit::sortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x00005647F73373F2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x00005647F733CC41 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x00007F10D9033D68 in /lib/x86_64-linux-gnu/libc.so.6 +90: 4# 0x00005631A31083F2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x00005631A310DC41 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x00007F87B242ED68 in /lib/x86_64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -90: 8# 0x00005647F733CD81 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 8# 0x00005631A310DD81 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: -90: [12:00:55] ------------------------------------- -90: [12:00:55] Test substructure matching with a pathological case for symmetric SSSR -90: [12:00:55] ------------------------------------- -90: [12:00:55] Test isAtomTerminalRGroupOrQueryHydrogen -73: [12:00:55] Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:00:55] ERROR: Could not sanitize molecule ending on line 21 -73: [12:00:55] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:00:55] Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:00:55] ERROR: Could not sanitize molecule ending on line 21 -73: [12:00:55] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:00:55] ERROR: Atom line too short: ' -9.6' on line 28 -73: [12:00:55] ERROR: moving to the beginning of the next molecule -73: [12:00:55] Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:00:55] ERROR: Could not sanitize molecule ending on line 21 -73: [12:00:55] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -73: [12:00:55] ERROR: Atom line too short: ' -9.6' on line 28 -73: [12:00:55] ERROR: moving to the beginning of the next molecule -73: [12:00:55] Finished: testGitHub2479() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -73: [12:00:55] -73: -73: **** -73: Invariant Violation -73: bad chiral bond -73: Violation occurred on line 161 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -73: Failed Expression: bnd -73: ---------- -73: Stacktrace: -73: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -73: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -73: 2# 0x00007F09C9595A1A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -73: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -73: 4# 0x0000555AD43E38CE in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 5# 0x0000555AD43E275B in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 6# 0x00007F09C8A33D68 in /lib/x86_64-linux-gnu/libc.so.6 -73: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -73: 8# 0x0000555AD43E29D1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: ---------- -73: **** -73: -73: [12:00:55] Finished: testGitHub2881() -73: [12:00:55] ----------------------------------------- -73: -73: [12:00:55] ----------------------------------------- -73: [12:00:55] Finished: testGitHub3517() -73: [12:00:55] ----------------------------------------- -73: -61: Test -61: -61: Sotorasib_atropBad2.cxsmi -61: -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -76: 0.40201265 0.40201265 -76: -0.13299436 -0.13299436 -76: 1.00000017 1.00000017 -76: 0.8762226 0.8762226 -76: 0.9973909 0.9973909 -76: 1.00000003 1.00000003 -76: 0.36613799 0.36613799 -76: 2.1107185 2.1107185 -76: 0.99999982 0.99999982 -76: 2.48696157 2.48696157 -76: 1.00479935 1.00479935 -76: 0.99999999 0.99999999 -76: 3.03311841 3.03311841 -76: 2.23739955 2.23739955 -76: 1.0000001 1.0000001 -76: 3.00772337 3.00772337 -76: 0.37399294 0.37399294 -76: 2.07713325 2.07713325 -76: 3.0077234 3.0077234 -76: 0.37399312 0.37399312 -76: -0.07713336 -0.07713336 -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 - 77/235 Test #73: testMolSupplier ........................ Passed 0.72 sec -test 119 - Start 119: testMORSE +90: [09:20:27] ------------------------------------- +90: [09:20:27] Test substructure matching with a pathological case for symmetric SSSR +90: [09:20:27] ------------------------------------- +90: [09:20:27] Test isAtomTerminalRGroupOrQueryHydrogen + 75/235 Test #90: testSubstructMatch ..................... Passed 0.85 sec +test 95 + Start 95: testEnumeration -119: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE -119: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -119: Test timeout computed to be: 1500 -76: [12:00:55] bond with order 0 found on line 11. This is not part of the MDL specification. -76: [12:00:55] bond with order 0 found on line 16. This is not part of the MDL specification. - 78/235 Test #90: testSubstructMatch ..................... Passed 0.56 sec -test 120 - Start 120: test3D +95: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration +95: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +95: Test timeout computed to be: 1500 +94: [09:20:27] ------------------------------------- +94: [09:20:27] Test Reaction StructuralFingerprint +94: [09:20:28] ------------------------------------- +94: [09:20:28] Test Reaction DifferenceFingerprint + 76/235 Test #94: testReactionFingerprints ............... Passed 0.08 sec +test 96 + Start 96: rxnTestCatch -120: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D -120: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -120: Test timeout computed to be: 1500 -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -61: [12:00:55] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -98: [12:00:55] == testCartesianProduct -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: .[12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -99: [12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -120: [12:00:55] ------------------------------------- -120: [12:00:55] Basic PMI tests. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: .[12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -99: [12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -99: [12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -99: [12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -99: [12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -99: [12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -99: [12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -99: [12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -99: [12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -99: [12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: [12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -99: [12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -99: [12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -99: [12:00:55] reactant 0 has no mapped atoms. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. +96: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch +96: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +96: Test timeout computed to be: 1500 +93: [09:20:28] 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 +96: Randomness seeded to: 3507555771 +96: [09:20:28] atom 0 in product 0 has multiple charge specifications. +96: [09:20:28] Found a SCD/SED line with missing/empty SDT specification at line 34 +96: [09:20:28] Found a SCD/SED line with missing/empty SDT specification at line 36 +96: [09:20:28] Found a SCD/SED line with missing/empty SDT specification at line 38 +96: [09:20:28] Found a SCD/SED line with missing/empty SDT specification at line 40 +96: [09:20:28] Found a SCD/SED line with missing/empty SDT specification at line 42 +96: [09:20:28] Found a SCD/SED line with missing/empty SDT specification at line 87 +96: [09:20:28] Found a SCD/SED line with missing/empty SDT specification at line 89 +96: [09:20:28] Found a SCD/SED line with missing/empty SDT specification at line 91 +96: [09:20:28] Found a SCD/SED line with missing/empty SDT specification at line 93 +96: [09:20:28] Found a SCD/SED line with missing/empty SDT specification at line 95 +96: [09:20:28] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [09:20:28] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [09:20:28] SMARTS Parse Error: unclosed ring for input: 'CC1' +96: [09:20:28] SMILES Parse Error: unclosed ring for input: 'CC1' +96: [09:20:28] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [09:20:28] product atom-mapping number 2 not found in reactants. +96: [09:20:28] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [09:20:28] product atom-mapping number 2 not found in reactants. +96: [09:20:28] CX Extensions: Substance group hierarchy is not always preserved. +96: [09:20:28] CX Extensions: Substance group hierarchy is not always preserved. +96: [09:20:28] reactant 0 has no mapped atoms. +96: [09:20:28] product 0 has no mapped atoms. +96: [09:20:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [09:20:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [09:20:28] Explicit valence for atom # 1 O, 5, is greater than permitted +96: =============================================================================== +96: All tests passed (722 assertions in 30 test cases) +96: + 77/235 Test #96: rxnTestCatch ........................... Passed 0.22 sec +test 97 + Start 97: pyChemReactions + +97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" +97: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +97: Test timeout computed to be: 1500 +93: [09:20:28] product atom-mapping number 17 not found in reactants. +93: [09:20:28] product atom-mapping number 18 not found in reactants. +93: [09:20:28] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 12 +91: Randomness seeded to: 1431405697 +91: =============================================================================== +91: All tests passed (242 assertions in 12 test cases) +91: +89: Randomness seeded to: 1500365237 +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. + 78/235 Test #91: substructTestCatch ..................... Passed 1.16 sec +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +test 98 + Start 98: pyChemReactionEnumerations + +98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" +98: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +98: Test timeout computed to be: 1500 +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +71: [09:20:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +71: [09:20:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +71: Atropisomers- 1 hits 3 misses +71: Final results: +71: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. + 79/235 Test #71: testAtropisomers ....................... Passed 2.60 sec +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +test 99 + Start 99: pyChemReactionSanitize + +99: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" +99: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +99: Test timeout computed to be: 1500 +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [09:20:28] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +93: [09:20:28] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: [09:20:28] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: +93: [09:20:28] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +93: ------------- +93: CCOc1ccccc1 +69: Test +69: +69: badWedgeError.sdf +69: +69: Test +69: +69: CrossedDoubleBondWithChiralNbr2.sdf +69: +69: Test +69: +69: CrossedDoubleBondWithChiralNbr.sdf +69: +69: Test +69: +69: SimpleWiggleDoubleBond.sdf +69: +69: Test +69: +69: lostStereoAnd.sdf +69: +69: Test +69: +69: DoubleBondChain.sdf +69: +69: Test +69: +69: UnitsError.sdf +69: +69: Test +69: +69: StarAtom.sdf +69: +69: Test +69: +69: nonProprietary.mol +69: +69: Test +69: +69: ChiralTest.sdf +69: +69: Test +69: +69: TestBond1.mol +69: +69: Test +69: +69: Sgroup_MUL_ParentInMiddle.sdf +69: +69: Test +69: +69: BadRxn.rxn +69: +69: Test +69: +69: FalseChiral.mrv +69: +69: Test +69: +69: FalseChiral.mrv +69: +69: Test +69: +69: Cubane.mrv +69: +69: Test +69: +69: NewChiralTest.mrv +69: +69: Test +69: +69: NewChiralTest.mrv +69: +69: Test +69: +69: NewChiralTestNoChiral.mrv +69: +69: Test +69: +69: NewChiralTestNoChiral.mrv +69: +69: Test +69: +69: NewChiralTestAllChiral.mrv +69: +69: Test +69: +69: NewChiralTestAllChiral.mrv +69: +69: Test +69: +69: DataSgroupMissingUnitsDisplayed.mrv +69: +69: Test +69: +69: lostStereoAnd.mrv +69: +69: Test +69: +69: DoubleBondChain.mrv +69: +69: Test +69: +69: WigglyAndCrossed.mrv +69: +69: Test +69: +69: BondTypes.mrv +69: +69: Test +69: +69: EmbeddedSGroupSUP_MUL.mrv +69: +69: Test +69: +69: EmbeddedSgroupCOP_SUP.mrv +69: +69: Test +69: +69: EmbeddedSgroupDAT_SUP.mrv +69: +69: Test +69: +69: EmbeddedSgroupMULTICENTER_SUP.mrv +69: +69: Test +69: +69: EmbeddedSgroupMUL_MUL.mrv +69: +69: Test +69: +69: EmbeddedSgroupMUL_MUL2.mrv +69: +69: Test +69: +69: EmbeddedSgroupMUL_SUP.mrv +69: +69: Test +69: +69: EmbeddedSgroupSRU_SUP.mrv +69: +69: Test +69: +69: EmbeddedSgroupSUPEXP_SUP.mrv +69: +69: Test +69: +69: EmbeddedSgroupSUPEXP_SUP2.mrv +69: +69: Test +69: +69: EmbeddedSgroupSUP_MULTICENTER.mrv +69: +69: Test +69: +69: EmbeddedSgroupSUP_SUP.mrv +69: +69: Test +69: +69: EmbeddedSgroupSUP_SUP2.mrv +69: +69: Test +69: +69: RgroupBad.mrv +69: +69: Test +69: +69: valenceLessThanDrawn.mrv +69: +69: Test +69: +69: data_sgroup_no_fieldname.mrv +69: +69: Test +69: +69: data_sgroup_empty_field_data.mrv +69: +69: Test +69: +69: radical_value.mrv +69: +69: Test +69: +69: emptyOneLineAtomList.mrv +69: +69: Test +69: +69: mrvValence_value.mrv +69: +69: Test +69: +69: ChiralTest2.mrv +69: +69: Test +69: +69: ChiralTest.mrv +69: +69: Test +69: +69: SnCl2.mrv +69: +69: Test +69: +69: SnH2Cl2.mrv +69: +69: Test +69: +69: marvin01.mrv +69: +69: Test +69: +69: marvin02.mrv +69: +69: Test +69: +69: marvin07.mrv +69: +69: Test +69: +69: marvin10.mrv +69: +69: Test +69: +69: marvin06.mrv +69: +69: Test +69: +69: marvin12.mrv +69: +69: Test +69: +69: EmptyMol.mrv +69: +69: Test +69: +69: Sparse.mrv +69: +69: Test +69: +69: Sparse2.mrv +69: +69: Test +69: +69: Sparse3.mrv +69: +69: Test +69: +69: MarvinNoCoords.mrv +69: +69: Test +69: +69: aspirin.mrv +69: +69: Test +69: +69: MarvinStereoGroupsZeros.mrv +69: +69: Test +69: +69: MarvinStereoGroupsAbs.mrv +69: +69: Test +69: +69: triphenylphosphine.mrv +69: +69: Test +69: +69: MarvinOldSuperGroupTest.mrv +69: +69: Test +69: +69: RadicalTests.mrv +69: +69: Test +69: +69: AnyBond.mrv +69: +69: Test +69: +69: cisBenzene.mrv +69: +69: Test +69: +69: DativeBond.mrv +69: +69: Test +69: +69: MultipleSgroup.mrv +69: +69: Test +69: +69: SgroupExpanded.mrv +69: +69: Test +69: +69: SgroupMultAttach.mrv +69: +69: Test +69: +69: MarvinMissingX2.mrv +69: +69: Test +69: +69: MarvinMissingY2.mrv +69: +69: Test +69: +69: DataSgroup.mrv +69: +69: Test +69: +69: MulticenterSgroup.mrv +69: +69: [09:20:28] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +69: [09:20:28] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +95: 30000000 30000000 +36: [09:20:28] Maximum BFS search size exceeded. +36: This is likely due to a highly symmetric fused ring system. +97: ...[09:20:28] +97: +97: **** +69: Test +69: +69: GenericSgroup.mrv +69: +69: Test +69: +69: MonomerSgroup.mrv +69: +69: Test +69: +69: modification_sgroup.mrv +69: +69: Test +69: +69: copolymer_sgroup.mrv +69: +69: Test +69: +69: MultipleSgroupParentInMiddleOfAtomBlock.mrv +69: +69: Test +69: +69: EmbeddedSgroups.mrv +69: +69: Test +69: +69: marvin03.mrv +69: +69: Test +69: +69: MarvinBadMissingMolID.mrv +69: +69: [09:20:28] +69: +69: **** +97: Pre-condition Violation +97: getNumImplicitHs() called without preceding call to calcImplicitValence() +97: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp +97: Failed Expression: d_implicitValence > -1 +97: ---------- +97: Stacktrace: +97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x00007F92AB44066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so +97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x00007F92A91B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x00007F92A91B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x00007F92A91B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x00007F92A91B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x00007F92A91B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x00007F92AB43D406 in /lib/x86_64-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# 0x00000000005BEE79 in /usr/bin/python3 +97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 51# 0x0000000000547080 in /usr/bin/python3 +97: 52# 0x00000000006AB720 in /usr/bin/python3 +97: 53# _PyObject_MakeTpCall in /usr/bin/python3 +97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 55# 0x00000000005BEE79 in /usr/bin/python3 +97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 57# 0x0000000000547080 in /usr/bin/python3 +97: 58# 0x00000000006AB720 in /usr/bin/python3 +97: 59# _PyObject_MakeTpCall in /usr/bin/python3 +97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 61# 0x00000000005BEE79 in /usr/bin/python3 +97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 63# 0x0000000000547080 in /usr/bin/python3 +97: 64# 0x00000000006AB720 in /usr/bin/python3 +97: 65# _PyObject_MakeTpCall in /usr/bin/python3 +97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 67# 0x0000000000595987 in /usr/bin/python3 +97: 68# _PyObject_MakeTpCall in /usr/bin/python3 +97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 70# PyEval_EvalCode in /usr/bin/python3 +97: 71# 0x000000000066A861 in /usr/bin/python3 +97: 72# 0x000000000066670C in /usr/bin/python3 +97: 73# 0x000000000067F713 in /usr/bin/python3 +97: 74# 0x000000000067ECE3 in /usr/bin/python3 +97: 75# 0x000000000067EB1E in /usr/bin/python3 +97: 76# Py_RunMain in /usr/bin/python3 +97: 77# Py_BytesMain in /usr/bin/python3 +97: 78# 0x00007F92ABE6ED68 in /lib/x86_64-linux-gnu/libc.so.6 +97: 79# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +97: 80# _start in /usr/bin/python3 +97: ---------- +97: **** +97: +97: [09:20:28] +97: +97: **** +69: Test Assert +69: Expression Failed: +69: Violation occurred on line 329 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp +69: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# 0x000055908DDBB99F in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +69: 3# 0x000055908DDC669C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +69: 4# 0x000055908DDB3A5D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +69: 5# 0x00007FBE2EC2ED68 in /lib/x86_64-linux-gnu/libc.so.6 +69: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +69: 7# 0x000055908DDB3BE1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +69: ---------- +69: **** +69: +69: Test +69: +69: MarvinBadMissingAtomID.mrv +69: +69: Expected id, elementType for an atom definition in MRV file +97: Pre-condition Violation +97: getNumImplicitHs() called without preceding call to calcImplicitValence() +97: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp +97: Failed Expression: d_implicitValence > -1 +97: ---------- +97: Stacktrace: +97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x00007F92AB44066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so +97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x00007F92A91B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x00007F92A91B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x00007F92A91B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x00007F92A91B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x00007F92A91B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x00007F92AB43D406 in /lib/x86_64-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# 0x00000000005BEE79 in /usr/bin/python3 +97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 51# 0x0000000000547080 in /usr/bin/python3 +97: 52# 0x00000000006AB720 in /usr/bin/python3 +97: 53# _PyObject_MakeTpCall in /usr/bin/python3 +97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 55# 0x00000000005BEE79 in /usr/bin/python3 +97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 57# 0x0000000000547080 in /usr/bin/python3 +97: 58# 0x00000000006AB720 in /usr/bin/python3 +97: 59# _PyObject_MakeTpCall in /usr/bin/python3 +97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 61# 0x00000000005BEE79 in /usr/bin/python3 +97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 63# 0x0000000000547080 in /usr/bin/python3 +97: 64# 0x00000000006AB720 in /usr/bin/python3 +97: 65# _PyObject_MakeTpCall in /usr/bin/python3 +97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 67# 0x0000000000595987 in /usr/bin/python3 +97: 68# _PyObject_MakeTpCall in /usr/bin/python3 +97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 70# PyEval_EvalCode in /usr/bin/python3 +97: 71# 0x000000000066A861 in /usr/bin/python3 +97: 72# 0x000000000066670C in /usr/bin/python3 +97: 73# 0x000000000067F713 in /usr/bin/python3 +97: 74# 0x000000000067ECE3 in /usr/bin/python3 +97: 75# 0x000000000067EB1E in /usr/bin/python3 +97: 76# Py_RunMain in /usr/bin/python3 +97: 77# Py_BytesMain in /usr/bin/python3 +97: 78# 0x00007F92ABE6ED68 in /lib/x86_64-linux-gnu/libc.so.6 +97: 79# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +97: 80# _start in /usr/bin/python3 +97: ---------- +97: **** +97: +69: Test +69: +69: MarvinBadX2.mrv +69: +69: The values x2 and y2 must be large floats in MRV file +69: Test +69: +69: MarvinBadY2.mrv +69: +69: The values x2 and y2 must be large floats in MRV file +69: Test +69: +69: MarvinBadStereoGroupsAbs.mrv +69: +69: Unrecognized group definition +69: Test +69: +69: MarvinBadElementType.mrv +69: +69: Test +69: +69: MarvinBadMissingBondID.mrv +69: +69: Test +69: +69: MarvinBadMissingBondAtomRefs +69: +69: Test +69: +69: MarvinBadMissingBondOrder.mrv +69: +69: bond must have one of: order, queryType, or convention in MRV File +69: Test +69: +69: MarvinBadMissingSruMolID.mrv +69: +69: Expected a molID in MRV file +97: .........[09:20:28] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [09:20:28] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [09:20:28] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [09:20:28] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: .[09:20:28] product atom-mapping number 1 found multiple times. +69: Test +69: +69: MarvinBadMissingSruID.mrv +69: +69: Test +69: +69: MarvinBadMissingSruRole.mrv +69: +69: Test +69: +69: MarvinBadMissingSruAtomRef.mrv +69: +69: Test +69: +69: MarvinBadMissingSruTitle.mrv +69: +69: Test +69: +69: MarvinBadSruAtomRef.mrv +69: +69: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +69: Test +69: +69: MarvinBadSruID.mrv +69: +69: Test +69: +69: MarvinBadSruRole.mrv +69: +69: Test +69: +69: MarvinBadSruAtomRef.mrv +69: +69: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +69: Test +69: +69: MarvinBadSruAtomRef.mrv +69: +69: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +97: [09:20:28] product atom-mapping number 1 found multiple times. +69: Test +69: +69: MarvinBadSruConnect.mrv +69: +69: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file +69: Test +69: +69: MarvinBadSupAttachAtom.mrv +69: +69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +69: Test +69: +69: MarvinBadSupAttachBond.mrv +69: +69: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file +69: Test +69: +69: MarvinBadSupAttachOrder.mrv +69: +69: Order for an AttachmentPoint definition must be an integer in MRV file +69: Test +69: +69: MarvinBadSupAttachAtom.mrv +69: +69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +69: Test +69: +69: MarvinBadSupAttachAtom.mrv +69: +69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +69: Test +69: +69: MarvinBadSupAttachAtom.mrv +69: +69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +69: Test +69: +69: MarvinBadSupMissingAttachBond.mrv +69: +69: No attachment point found for bond to the condensed atom in a superatomSgroup +69: Test +69: +69: MarvinBadSupMissingAttachOrder.mrv +69: +69: Expected atom, order and bond, for an AttachmentPoint definition in MRV file +36: F/C=C/Cl +36: [H]/C(F)=C(/[H])Cl +36: F/C=C/Cl +36: F/C=C/Cl +36: C/C(F)=C(/C)Cl +97: ................[09:20:29] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: [09:20:29] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +97: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +97: [09:20:29] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: ..[09:20:29] reactant 2 has no mapped atoms. +97: [09:20:29] reactant 2 has no mapped atoms. +97: [09:20:29] product 1 has no mapped atoms. +36: [09:20:29] ----------------------- +36: Testing isRingFused +97: ........[09:20:29] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +97: [09:20:29] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +97: [09:20:29] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +97: [09:20:29] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +97: .[09:20:29] reactant atom-mapping number 1 found multiple times. +97: [09:20:29] product atom-mapping number 2 not found in reactants. +97: [09:20:29] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 4 +97: [09:20:29] product atom-mapping number 5 not found in reactants. + 80/235 Test #36: graphmolMolOpsTest ..................... Passed 4.41 sec +test 100 + Start 100: testChemTransforms + +100: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms +100: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms +100: Test timeout computed to be: 1500 +97: ........./build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.6/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: 1 smi: CC +100: 1 smi: CC +100: 2 smi: CCO[C@H](N)P +100: 2 smi: CC +100: replaceSub smi1:CCP(CC)[C@@H](N)O +100: replaceSub smi1:CCNCC +100: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O +100: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O +97: [09:20:29] Found a SCD/SED line with missing/empty SDT specification at line 34 +97: [09:20:29] Found a SCD/SED line with missing/empty SDT specification at line 36 +97: [09:20:29] Found a SCD/SED line with missing/empty SDT specification at line 38 +97: [09:20:29] Found a SCD/SED line with missing/empty SDT specification at line 40 +97: [09:20:29] Found a SCD/SED line with missing/empty SDT specification at line 42 +97: [09:20:29] Found a SCD/SED line with missing/empty SDT specification at line 87 +97: [09:20:29] Found a SCD/SED line with missing/empty SDT specification at line 89 +97: [09:20:29] Found a SCD/SED line with missing/empty SDT specification at line 91 +97: [09:20:29] Found a SCD/SED line with missing/empty SDT specification at line 93 +97: [09:20:29] Found a SCD/SED line with missing/empty SDT specification at line 95 +69: Test +69: +69: marvin03.mrv +69: +69: Test +69: +69: Cubane.mrv +69: +69: Test +69: +69: FalseAtropisomer.mrv +69: +69: Test +69: +69: AtropEnhancedStereo.mrv +69: +69: Test +69: +69: AtropManyChirals.mrv +69: +69: Test +69: +69: AtropManyChiralsEnhanced.mrv +69: +69: Test +69: +69: AtropManyChiralsEnhanced2.mrv +69: +69: Test +69: +69: AtropManyChiralsEnhanced3.mrv +69: +69: Test +69: +69: AtropManyChiralsEnhanced4.mrv +69: +69: Test +69: +69: BMS-986142_3d_chiral.mrv +69: +69: Test +69: +69: BMS-986142_3d.mrv +69: +69: Test +69: +69: BMS-986142_atrop1.mrv +69: +69: Test +69: +69: BMS-986142_atrop2.mrv +69: +69: Test +69: +69: BMS-986142_atrop3.mrv +69: +69: Test +69: +69: BMS-986142_atrop4.mrv +69: +69: Test +69: +69: BMS-986142_atrop5.mrv +69: +69: [09:20:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [09:20:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +97: ..[09:20:29] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [09:20:29] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [09:20:29] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [09:20:29] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [09:20:29] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [09:20:29] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [09:20:29] reaction has no reactants +97: [09:20:29] reaction has no products +97: [09:20:29] initialization failed +97: [09:20:29] reaction has no reactants +97: [09:20:29] reaction has no products +69: Test +69: +69: BMS-986142_atrop6.mrv +69: +69: Test +69: +69: BMS-986142_atrop7.mrv +69: +69: Test +69: +69: BMS-986142_atrop8.mrv +69: +69: [09:20:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [09:20:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +100: [09:20:29] SMARTS Parse Error: syntax error while parsing: bar +100: [09:20:29] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' +97: .[09:20:29] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [09:20:29] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [09:20:29] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [09:20:29] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [09:20:29] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [09:20:29] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [09:20:29] reaction has no reactants +97: [09:20:29] reaction has no products +97: [09:20:29] initialization failed +97: [09:20:29] reaction has no reactants +97: [09:20:29] reaction has no products +97: . +97: ---------------------------------------------------------------------- +97: Ran 54 tests in 0.604s +97: +97: OK +69: Test +69: +69: BMS-986142_atropBad2.mrv +69: +69: [09:20:29] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +97: ******************************************** +97: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +97: +69: Test +69: +69: JDQ443_3d.mrv +69: +69: Test +69: +69: JDQ443_atrop1.mrv +69: +69: Test +69: +69: JDQ443_atrop2.mrv +69: +69: Test +69: +69: JDQ443_atrop3.mrv +69: +69: Test +69: +69: JDQ443_atropBad1.mrv +69: +69: [09:20:29] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +69: Test +69: +69: RP-6306_atrop1.mrv +69: +69: Test +69: +69: RP-6306_atrop2.mrv +69: +69: Test +69: +69: RP-6306_atrop3.mrv +69: +69: Test +69: +69: RP-6306_atrop4.mrv +69: +69: Test +69: +69: RP-6306_atrop5.mrv +69: +69: [09:20:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [09:20:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored + 81/235 Test #100: testChemTransforms ..................... Passed 0.55 sec +test 101 + Start 101: chemTransformsTestCatch + +101: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms +101: Test timeout computed to be: 1500 +93: [09:20:29] reactant 0 has no mapped atoms. +93: [09:20:29] product 0 has no mapped atoms. +93: [09:20:29] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. +69: Test +69: +69: RP-6306_atropBad1.mrv +69: +69: [09:20:29] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +69: Test +69: +69: RP-6306_atropBad2.mrv +69: +69: [09:20:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [09:20:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [09:20:29] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 + 82/235 Test #93: testReaction ........................... Passed 2.17 sec +test 102 + Start 102: tautomerQueryTestCatch + +102: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch +102: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery +102: Test timeout computed to be: 1500 +101: Randomness seeded to: 994563225 +101: [09:20:29] Incomplete atom labelling, cannot make bond +101: [09:20:29] +101: +101: **** +101: Invariant Violation +101: molzip: bond info already exists for end atom with label:1 +101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +101: Failed Expression: !bond.b +101: ---------- +101: Stacktrace: +101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 4# 0x0000564B8C2A5256 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000564B8C2F6FE8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000564B8C2F7B08 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000564B8C2F7F80 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000564B8C2C9783 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000564B8C2C9AEC in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000564B8C29963E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F487BA2ED68 in /lib/x86_64-linux-gnu/libc.so.6 +101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +101: 13# 0x0000564B8C299681 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: ---------- +101: **** +101: +101: [09:20:29] Incomplete atom labelling, cannot make bond +101: [09:20:29] +101: +101: **** +101: Invariant Violation +101: molzip: bond info already exists for end atom with label:1 +101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +101: Failed Expression: !bond.b +101: ---------- +101: Stacktrace: +101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 4# 0x0000564B8C2A5256 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000564B8C2F6FE8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000564B8C2F7B08 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000564B8C2F7F80 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000564B8C2C9783 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000564B8C2C9AEC in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000564B8C29963E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F487BA2ED68 in /lib/x86_64-linux-gnu/libc.so.6 +101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +101: 13# 0x0000564B8C299681 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: ---------- +101: **** +101: +69: Test +69: +69: RP-6306_3d.mrv +69: +69: Test +69: +69: Sotorasib_atrop1.mrv +69: +69: Test +69: +69: Sotorasib_atrop2.mrv +69: +69: Test +69: +69: Sotorasib_atrop3.mrv +69: +69: Test +69: +69: Sotorasib_atrop4.mrv +69: +69: Test +69: +69: Sotorasib_atrop5.mrv +69: +69: [09:20:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [09:20:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +101: [09:20:29] Incomplete atom labelling, cannot make bond +101: [09:20:29] +101: +101: **** +101: Invariant Violation +101: molzip: bond info already exists for end atom with label:1 +101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +101: Failed Expression: !bond.b +101: ---------- +101: Stacktrace: +101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 4# 0x0000564B8C2A5256 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000564B8C2F6FE8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000564B8C2F7B08 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000564B8C2F7F80 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000564B8C2C9783 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000564B8C2C9AEC in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000564B8C29963E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F487BA2ED68 in /lib/x86_64-linux-gnu/libc.so.6 +101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +101: 13# 0x0000564B8C299681 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: ---------- +101: **** +101: +69: Test +69: +69: Sotorasib_atropBad1.mrv +69: +69: [09:20:29] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +101: [09:20:29] Incomplete atom labelling, cannot make bond +101: [09:20:29] Incomplete atom labelling, cannot make bond +101: [09:20:29] Incomplete atom labelling, cannot make bond +101: [09:20:29] +101: +101: **** +101: Invariant Violation +101: molzip: bond info already exists for end atom with label:1 +101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +101: Failed Expression: !bond.b +101: ---------- +101: Stacktrace: +101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 4# 0x0000564B8C2A5256 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000564B8C2F6FE8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000564B8C2F7B08 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000564B8C2F7F80 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000564B8C2C9783 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000564B8C2C9AEC in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000564B8C29963E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F487BA2ED68 in /lib/x86_64-linux-gnu/libc.so.6 +101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +101: 13# 0x0000564B8C299681 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: ---------- +101: **** +101: +69: Test +69: +69: Sotorasib_atropBad2.mrv +69: +69: [09:20:29] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +101: [09:20:29] Incomplete atom labelling, cannot make bond +101: [09:20:29] +101: +101: **** +101: Invariant Violation +101: molzip: bond info already exists for end atom with label:1 +101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +101: Failed Expression: !bond.b +101: ---------- +101: Stacktrace: +101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 4# 0x0000564B8C2A5256 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000564B8C2F6FE8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000564B8C2F7B08 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000564B8C2F7F80 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000564B8C2C9783 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000564B8C2C9AEC in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000564B8C29963E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007F487BA2ED68 in /lib/x86_64-linux-gnu/libc.so.6 +101: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +101: 13# 0x0000564B8C299681 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: ---------- +101: **** +101: +101: [09:20:29] +101: +101: **** +101: Invariant Violation +101: molzip: zipped Bond already exists, perhaps labels are duplicated +101: Violation occurred on line 735 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +101: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) +101: ---------- +101: Stacktrace: +101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 5# 0x0000564B8C29A43D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000564B8C2F6FE8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000564B8C2F7B08 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000564B8C2F7F80 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000564B8C2C9783 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000564B8C2C9AEC in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000564B8C29963E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 12# 0x00007F487BA2ED68 in /lib/x86_64-linux-gnu/libc.so.6 +101: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +101: 14# 0x0000564B8C299681 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: ---------- +101: **** +101: +101: =============================================================================== +101: All tests passed (674 assertions in 9 test cases) +101: + 83/235 Test #97: pyChemReactions ........................ Passed 1.73 sec +test 103 + Start 103: pyTautomerQuery + +103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" +103: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap +103: Test timeout computed to be: 1500 + 84/235 Test #101: chemTransformsTestCatch ................ Passed 0.36 sec +test 104 + Start 104: testSubgraphs1 + +104: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 +104: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +104: Test timeout computed to be: 1500 +99: .[09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: .[09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. 99: () 99: ******************************************** 99: $RXN @@ -22487,39 +23231,17 @@ 99: 1 2 1 0 99: M ISO 2 1 1 2 2 99: M END -99: [12:00:55] reactant 0 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] product 0 has no mapped atoms. -99: [12:00:55] Could not find RLabel mapping for atom: 0 in template: 1 -99: [12:00:55] reactant 1 has no mapped atoms. - 79/235 Test #76: testMolWriter .......................... Passed 0.76 sec -111: [12:00:55] done -111: [12:00:55] ------------------------------------- -111: [12:00:55] Test VSA descriptors. -test 121 - Start 121: testWHIM - -121: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM -121: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -121: Test timeout computed to be: 1500 -111: [12:00:55] done -111: [12:00:55] ------------------------------------- -111: [12:00:55] Test molecular formula calculation. -111: [12:00:55] done -111: [12:00:55] ------------------------------------- -111: [12:00:55] Test Issue 3415534. -111: [12:00:55] done -111: [12:00:55] ------------------------------------- -111: [12:00:55] Test Issue3433771: Bad definition for Crippen atom type O11. -111: [12:00:55] done -111: [12:00:55] ------------------------------------- -111: [12:00:55] Test multithreading -111: reading molecules -99: [12:00:55] reactant 1 has no mapped atoms. -99: [12:00:55] reactant 1 has no mapped atoms. +99: [09:20:30] reactant 0 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] product 0 has no mapped atoms. +99: [09:20:30] Could not find RLabel mapping for atom: 0 in template: 1 +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +99: [09:20:30] reactant 1 has no mapped atoms. +98: [09:20:30] == testCartesianProduct 99: .. 99: ---------------------------------------------------------------------- -99: Ran 4 tests in 0.041s +99: Ran 4 tests in 0.104s 99: 99: OK 99: @@ -22576,176 +23298,219 @@ 99: M END 99: 99: $RXN Failed -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[12:00:55] == testEnumerateLibrary -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -93: [12:00:55] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: [12:00:55] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -93: [12:00:55] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.6/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 -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -93: ------------- -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: Atropisomers- 1 hits 3 misses -71: Final results: -71: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -93: CCOc1ccccc1 - 80/235 Test #71: testAtropisomers ....................... Passed 0.83 sec -test 122 - Start 122: testGETAWAY - -122: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY -122: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -122: Test timeout computed to be: 1500 -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: processing -111: launch :0 -111: launch :1 -111: launch :2 -111: launch :3 -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -30: ... -30: ---------------------------------------------------------------------- -30: Ran 12 tests in 0.657s -30: -30: OK -61: Test -61: -61: Sotorasib_3d.cxsmi -61: -61: Test -61: -61: ZM374979_atrop1.cxsmi -61: -61: Test -61: -61: ZM374979_atrop2.cxsmi -61: -61: Test -61: -61: ZM374979_atrop3.cxsmi -61: -61: Test -61: -61: ZM374979_atrop4.cxsmi -61: -61: Test -61: -61: ZM374979_atropBad1.cxsmi -61: -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -102: Randomness seeded to: 1957632728 +104: ----------------------- +104: Subgraph retrieval +104: Finished +104: ----------------------- +104: testSubgraphs2a +104: Finished +104: ----------------------- +104: testSubgraphs2 +69: Test +69: +69: Sotorasib_3d.mrv +69: +69: Test +69: +69: ZM374979_atrop1.mrv +69: +69: Test +69: +69: ZM374979_atrop2.mrv +69: +69: Test +69: +69: ZM374979_atrop3.mrv +69: +69: Test +69: +69: ZM374979_atropBad1.mrv +69: +69: [09:20:30] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +98: .[09:20:30] == testEnumerateLibrary +102: Randomness seeded to: 1463514185 102: =============================================================================== 102: All tests passed (93 assertions in 13 test cases) 102: -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 - 81/235 Test #102: tautomerQueryTestCatch ................. Passed 0.62 sec -test 123 - Start 123: testAUTOCORR3D + 85/235 Test #102: tautomerQueryTestCatch ................. Passed 0.42 sec +test 105 + Start 105: testSubgraphs2 -123: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D -123: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -123: Test timeout computed to be: 1500 -61: [12:00:55] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 82/235 Test #66: testDepictor ........................... Passed 0.93 sec -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 124 - Start 124: testCoulombMat +105: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 +105: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +105: Test timeout computed to be: 1500 +98: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.6/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 +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 +70: [09:20:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [09:20:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [09:20:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [09:20:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +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 + 86/235 Test #105: testSubgraphs2 ......................... Passed 0.08 sec +test 106 + Start 106: subgraphsCatch -124: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat -124: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -124: Test timeout computed to be: 1500 -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 100 -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: ..[12:00:55] == testRGroupState -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -124: ===================== Testing CoulombMat ======================= -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[12:00:55] == testRandomEnumerateAllBBsLibrary -98: ** [1, 1] -98: ** [0, 2] -98: ** [1, 0] -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -124: CM test 1 mat Done - 83/235 Test #99: pyChemReactionSanitize ................. Passed 0.71 sec -test 125 - Start 125: descriptorsTestCatch +106: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch +106: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +106: Test timeout computed to be: 1500 +70: [09:20:30] deprecated group abbreviation ignored on line 24 +92: Randomness seeded to: 1702661111 +92: =============================================================================== +92: All tests passed (11480 assertions in 38 test cases) +92: + 87/235 Test #92: testGenericGroups ...................... Passed 2.96 sec +test 107 + Start 107: filterCatalogTest -125: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch -125: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -125: Test timeout computed to be: 1500 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 84/235 Test #124: testCoulombMat ......................... Passed 0.07 sec -test 126 - Start 126: pyMolDescriptors +107: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest +107: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog +107: Test timeout computed to be: 1500 +70: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +69: Test +69: +69: mrtx1719_3d.mrv +69: +69: Test +69: +69: mrtx1719_atrop1.mrv +69: +69: Test +69: +69: mrtx1719_atrop2.mrv +69: +69: Test +69: +69: mrtx1719_atrop3.mrv +69: +69: Test +69: +69: mrtx1719_atropBad1.mrv +69: +69: [09:20:30] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [09:20:30] +70: +70: **** +70: Post-condition Violation +70: Element 'Mv' not found +70: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +70: Failed Expression: anum > -1 +70: ---------- +70: Stacktrace: +70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +70: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 3# 0x00007F4963EC8391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 4# 0x00007F4963ED1CFA in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 5# 0x00007F4963ED207D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 9# 0x000055CEEDDE8CF5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 10# 0x000055CEEDE4F4F2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 11# 0x000055CEEDDCF963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 12# 0x00007F496342ED68 in /lib/x86_64-linux-gnu/libc.so.6 +70: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +70: 14# 0x000055CEEDDCFB11 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: ---------- +70: **** +70: +106: Randomness seeded to: 862100844 +106: --------- +106: =============================================================================== +106: All tests passed (11 assertions in 1 test case) +106: + 88/235 Test #106: subgraphsCatch ......................... Passed 0.08 sec +test 108 + Start 108: pyFilterCatalog -126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" -126: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap -126: Test timeout computed to be: 1500 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -91: Randomness seeded to: 3713521452 -91: =============================================================================== -91: All tests passed (242 assertions in 12 test cases) -91: -98: .[12:00:56] == testRandomEnumerateLibrary -112: [12:00:56] done -112: [12:00:56] ------------------------------------- -112: [12:00:56] Test Github #3806: NaNs from AUTOCORR2D descriptor -112: [12:00:56] done +108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" +108: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap +108: Test timeout computed to be: 1500 +107: Warning: molecule failed filter +107: Warning: molecule failed filter: reason hzone_phenol_A(479) +107: v = { +107: 0,23}, +107: 1,22}, +107: 2,20}, +107: 3,19}, +107: 4,25}, +107: 5,24}, +107: 6,18}, +107: 7,17}, +107: 8,16}, +107: 9,21}, +107: } +107: match = { +107: 0,23}, +107: 1,22}, +107: 2,20}, +107: 3,19}, +107: 4,25}, +107: 5,24}, +107: 6,18}, +107: 7,17}, +107: 8,16}, +107: 9,21}, +107: } +107: Warning: molecule failed filter +107: Warning: molecule failed filter: reason cyano_imine_B(17) +107: v = { +107: 0,11}, +107: 1,12}, +107: 2,13}, +107: 3,14}, +107: 4,15}, +107: 5,10}, +107: 6,9}, +107: 7,8}, +107: 8,7}, +107: 9,6}, +107: 10,5}, +107: 11,17}, +107: 12,16}, +107: } +107: match = { +107: 0,11}, +107: 1,12}, +107: 2,13}, +107: 3,14}, +107: 4,15}, +107: 5,10}, +107: 6,9}, +107: 7,8}, +107: 8,7}, +107: 9,6}, +107: 10,5}, +107: 11,17}, +107: 12,16}, +107: } 104: Finished 104: ----------------------- 104: testRootedSubgraphs @@ -22753,434 +23518,1719 @@ 104: ----------------------- 104: testRootedPaths 104: Finished - 85/235 Test #112: testAUTOCORR2D ......................... Passed 0.55 sec - 86/235 Test #104: testSubgraphs1 ......................... Passed 0.69 sec -test 127 - Start 127: pyMolDescriptors3D - -127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/test3D.py" -127: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap -127: Test timeout computed to be: 1500 -test 128 - Start 128: testFingerprints - -128: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints -128: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -128: Test timeout computed to be: 1500 -116: [12:00:56] done -116: [12:00:56] ------------------------------------- -116: [12:00:56] PBF edge cases. -116: [12:00:56] done -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 87/235 Test #91: substructTestCatch ..................... Passed 0.79 sec - 88/235 Test #116: testPBF ................................ Passed 0.47 sec -test 129 - Start 129: testMHFPFingerprint - -129: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint -129: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -129: Test timeout computed to be: 1500 -test 130 - Start 130: testFingerprintGenerators + 89/235 Test #104: testSubgraphs1 ......................... Passed 0.41 sec +test 109 + Start 109: testFragCatalog -130: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators -130: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -130: Test timeout computed to be: 1500 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 89/235 Test #30: pyForceFieldConstraints ................ Passed 1.33 sec +109: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog +109: Test timeout computed to be: 1500 +107: Warning: molecule failed filter +107: Warning: molecule failed filter: reason keto_keto_gamma(5) +107: v = { +107: 0,0}, +107: 1,1}, +107: 2,2}, +107: 3,4}, +107: 4,5}, +107: 5,6}, +107: 6,7}, +107: 7,8}, +107: 8,9}, +107: 9,14}, +107: 10,15}, +107: 11,16}, +107: } +107: match = { +107: 0,0}, +107: 1,1}, +107: 2,2}, +107: 3,4}, +107: 4,5}, +107: 5,6}, +107: 6,7}, +107: 7,8}, +107: 8,9}, +107: 9,14}, +107: 10,15}, +107: 11,16}, +107: } +98: ..[09:20:30] == testRGroupState 61: Test 61: -61: Mrtx1719_3d.cxsmi +61: AtropCanon1.cxsmi 61: 61: Test 61: -61: Mrtx1719_atrop1.cxsmi +61: AtropCanon2.cxsmi 61: 61: Test 61: -61: Mrtx1719_atrop2.cxsmi +61: AtropCanon3.cxsmi 61: 61: Test 61: -61: Mrtx1719_atrop3.cxsmi +61: BMS-986142_3d_chiral.cxsmi 61: 61: Test 61: -61: Mrtx1719_atrop4.cxsmi -61: -61: Test +61: BMS-986142_3d.cxsmi 61: -61: Mrtx1719_atropBad1.cxsmi +61: =============================================================================== +61: All tests passed (2445 assertions in 29 test cases) 61: -61: [12:00:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -test 131 - Start 131: fpTestCatch + 90/235 Test #61: cxsmilesTest ........................... Passed 4.99 sec +98: .[09:20:30] == testRandomEnumerateAllBBsLibrary +test 110 + Start 110: pyFragCatalog -131: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch -131: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -131: Test timeout computed to be: 1500 -61: [12:00:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -61: [12:00:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -61: [12:00:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -61: [12:00:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -98: .[12:00:56] == testRandomSample -129: [12:00:56] ------------------------------------- -129: [12:00:56] Test MHFP fingerprint encoder initialization -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[12:00:56] == testRandomSampleAllBBs -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[12:00:56] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: [12:00:56] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead - 90/235 Test #107: filterCatalogTest ...................... Passed 0.72 sec -test 132 - Start 132: fpGenTestCatch +110: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap/rough_test.py" +110: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap +110: Test timeout computed to be: 1500 + 91/235 Test #99: pyChemReactionSanitize ................. Passed 1.95 sec +test 111 + Start 111: testDescriptors -132: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch -132: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -132: Test timeout computed to be: 1500 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors +111: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +111: Test timeout computed to be: 1500 +98: ** [1, 1] +98: ** [0, 2] +98: ** [1, 0] +109: 21 +111: [09:20:30] ------------------------------------- +111: [09:20:30] Test Crippen parameter acquisition. +111: [09:20:30] done +111: [09:20:30] ------------------------------------- +111: [09:20:30] Test Crippen calculation. +111: [09:20:30] done +111: [09:20:30] ------------------------------------- +111: [09:20:30] Test Issue262: problems with Crippen calculation from pickles. +111: [09:20:30] done +111: [09:20:30] ------------------------------------- +111: [09:20:30] Test AMW calculation. +111: [09:20:30] done +111: [09:20:30] ------------------------------------- +111: [09:20:30] Test Exact MW calculation. +111: [09:20:30] done +111: [09:20:30] ------------------------------------- +111: [09:20:30] Test Labute ASA descriptors. +111: [09:20:30] done +111: [09:20:30] ------------------------------------- +111: [09:20:30] Test TPSA descriptors. +98: .[09:20:30] == testRandomEnumerateLibrary +111: [09:20:30] done +111: [09:20:30] ------------------------------------- +111: [09:20:30] Test Lipinski parameters. +70: [09:20:30] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +70: [09:20:30] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +98: .[09:20:30] == testRandomSample +98: .[09:20:30] == testRandomSampleAllBBs 69: Test 69: -69: badWedgeError.sdf +69: FalseAtropisomer.mrv 69: 69: Test 69: -69: CrossedDoubleBondWithChiralNbr2.sdf +69: AtropEnhancedStereo.mrv 69: 69: Test 69: -69: CrossedDoubleBondWithChiralNbr.sdf +69: AtropManyChirals.mrv 69: 69: Test 69: -69: SimpleWiggleDoubleBond.sdf +69: AtropManyChiralsEnhanced.mrv 69: 69: Test 69: -69: lostStereoAnd.sdf +69: AtropManyChiralsEnhanced2.mrv 69: 69: Test 69: -69: DoubleBondChain.sdf +69: AtropManyChiralsEnhanced3.mrv 69: 69: Test 69: -69: UnitsError.sdf +69: AtropManyChiralsEnhanced4.mrv 69: 69: Test 69: -69: StarAtom.sdf +69: BMS-986142_3d_chiral.mrv 69: 69: Test 69: -69: nonProprietary.mol +69: BMS-986142_3d.mrv 69: 69: Test 69: -69: ChiralTest.sdf +69: BMS-986142_atrop1.mrv 69: 69: Test 69: -69: TestBond1.mol +69: BMS-986142_atrop2.mrv 69: 69: Test 69: -69: Sgroup_MUL_ParentInMiddle.sdf +69: BMS-986142_atrop3.mrv 69: 69: Test 69: -69: BadRxn.rxn +69: BMS-986142_atrop4.mrv 69: 69: Test 69: -69: FalseChiral.mrv +69: BMS-986142_atrop5.mrv 69: +69: [09:20:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [09:20:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +98: .[09:20:30] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: [09:20:30] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: .[09:20:30] == testRemoveBadMatches +98: .[09:20:30] == testTimings +111: [09:20:30] done +111: [09:20:30] ------------------------------------- +111: [09:20:30] Test VSA descriptors. +111: [09:20:30] done +111: [09:20:30] ------------------------------------- +111: [09:20:30] Test molecular formula calculation. +111: [09:20:30] done +111: [09:20:30] ------------------------------------- +111: [09:20:30] Test Issue 3415534. +111: [09:20:30] done +111: [09:20:30] ------------------------------------- +111: [09:20:30] Test Issue3433771: Bad definition for Crippen atom type O11. +111: [09:20:30] done +111: [09:20:30] ------------------------------------- +111: [09:20:30] Test multithreading +111: reading molecules 69: Test 69: -69: FalseChiral.mrv +69: BMS-986142_atrop6.mrv 69: 69: Test 69: -69: Cubane.mrv +69: BMS-986142_atrop7.mrv 69: 69: Test 69: -69: NewChiralTest.mrv +69: BMS-986142_atrop8.mrv 69: +69: [09:20:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [09:20:30] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: Test 69: -69: NewChiralTest.mrv +69: BMS-986142_atropBad2.mrv 69: +69: [09:20:30] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +111: processing +111: launch :0 +111: launch :1 +111: launch :2 +111: launch :3 +70: ---------------------------------- +70: ---------------------------------- +70: [09:20:30] +70: +70: **** +70: Pre-condition Violation +70: rlabel out of range for MDL files +70: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp +70: Failed Expression: rlabel >= 0 && rlabel < 100 +70: ---------- +70: Stacktrace: +70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +70: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +70: 3# 0x000055CEEDDF60FF in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 4# 0x000055CEEDE4F56A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 5# 0x000055CEEDDCF963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 6# 0x00007F496342ED68 in /lib/x86_64-linux-gnu/libc.so.6 +70: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +70: 8# 0x000055CEEDDCFB11 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: ---------- +70: **** +70: + 92/235 Test #107: filterCatalogTest ...................... Passed 0.72 sec +test 112 + Start 112: testAUTOCORR2D + +112: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D +112: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +112: Test timeout computed to be: 1500 +70: [09:20:30] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +103: ..... +103: ---------------------------------------------------------------------- +103: Ran 5 tests in 0.189s +103: +103: OK 69: Test 69: -69: NewChiralTestNoChiral.mrv +69: JDQ443_3d.mrv 69: 69: Test 69: -69: NewChiralTestNoChiral.mrv +69: JDQ443_atrop1.mrv 69: 69: Test 69: -69: NewChiralTestAllChiral.mrv +69: JDQ443_atrop2.mrv 69: 69: Test 69: -69: NewChiralTestAllChiral.mrv +69: JDQ443_atrop3.mrv 69: 69: Test 69: -69: DataSgroupMissingUnitsDisplayed.mrv +69: JDQ443_atropBad1.mrv 69: +69: [09:20:30] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +112: [09:20:31] ---------------------------- +112: start test autocorr2D 69: Test 69: -69: lostStereoAnd.mrv +69: RP-6306_atrop1.mrv 69: 69: Test 69: -69: DoubleBondChain.mrv +69: RP-6306_atrop2.mrv 69: 69: Test 69: -69: WigglyAndCrossed.mrv +69: RP-6306_atrop3.mrv 69: 69: Test 69: -69: BondTypes.mrv +69: RP-6306_atrop4.mrv 69: 69: Test 69: -69: EmbeddedSGroupSUP_MUL.mrv +69: RP-6306_atrop5.mrv 69: +69: [09:20:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [09:20:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: Test 69: -69: EmbeddedSgroupCOP_SUP.mrv +69: RP-6306_atropBad1.mrv 69: +69: [09:20:31] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 69: Test 69: -69: EmbeddedSgroupDAT_SUP.mrv +69: RP-6306_atropBad2.mrv 69: +69: [09:20:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [09:20:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [09:20:31] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. 69: Test 69: -69: EmbeddedSgroupMULTICENTER_SUP.mrv +69: RP-6306_3d.mrv 69: 69: Test 69: -69: EmbeddedSgroupMUL_MUL.mrv +69: Sotorasib_atrop1.mrv 69: 69: Test 69: -69: EmbeddedSgroupMUL_MUL2.mrv +69: Sotorasib_atrop2.mrv 69: 69: Test 69: -69: EmbeddedSgroupMUL_SUP.mrv +69: Sotorasib_atrop3.mrv 69: 69: Test 69: -69: EmbeddedSgroupSRU_SUP.mrv +69: Sotorasib_atrop4.mrv 69: 69: Test 69: -69: EmbeddedSgroupSUPEXP_SUP.mrv +69: Sotorasib_atrop5.mrv 69: +69: [09:20:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [09:20:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored + 93/235 Test #103: pyTautomerQuery ........................ Passed 1.27 sec +test 113 + Start 113: testATF + +113: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF +113: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +113: Test timeout computed to be: 1500 69: Test 69: -69: EmbeddedSgroupSUPEXP_SUP2.mrv +69: Sotorasib_atropBad1.mrv 69: +69: [09:20:31] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 69: Test 69: -69: EmbeddedSgroupSUP_MULTICENTER.mrv +69: Sotorasib_atropBad2.mrv 69: +69: [09:20:31] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +89: [09:20:31] Explicit valence for atom # 9 N, 6, is greater than permitted + 94/235 Test #113: testATF ................................ Passed 0.08 sec +test 114 + Start 114: testBCUT + +114: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT +114: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +114: Test timeout computed to be: 1500 +114: [09:20:31] ------------------------------------- +114: [09:20:31] Basic BCUT tests. +114: [09:20:31] done +114: [09:20:31] ------------------------------------- +114: [09:20:31] Larger BCUT tests. 69: Test 69: -69: EmbeddedSgroupSUP_SUP.mrv +69: Sotorasib_3d.mrv 69: 69: Test 69: -69: EmbeddedSgroupSUP_SUP2.mrv +69: ZM374979_atrop1.mrv 69: 69: Test 69: -69: RgroupBad.mrv +69: ZM374979_atrop2.mrv 69: 69: Test 69: -69: valenceLessThanDrawn.mrv +69: ZM374979_atrop3.mrv 69: 69: Test 69: -69: data_sgroup_no_fieldname.mrv +69: ZM374979_atropBad1.mrv 69: +69: [09:20:31] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +110: ......... +110: ---------------------------------------------------------------------- +110: Ran 9 tests in 0.180s +110: +110: OK 69: Test 69: -69: data_sgroup_empty_field_data.mrv +69: mrtx1719_3d.mrv 69: 69: Test 69: -69: radical_value.mrv +69: mrtx1719_atrop1.mrv 69: 69: Test 69: -69: emptyOneLineAtomList.mrv +69: mrtx1719_atrop2.mrv 69: 69: Test 69: -69: mrvValence_value.mrv +69: mrtx1719_atrop3.mrv 69: 69: Test 69: -69: ChiralTest2.mrv +69: mrtx1719_atropBad1.mrv +69: +69: [09:20:31] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [09:20:31] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +70: [09:20:31] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' + 95/235 Test #110: pyFragCatalog .......................... Passed 1.29 sec +test 115 + Start 115: testEEM + +115: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM +115: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +115: Test timeout computed to be: 1500 +112: [09:20:32] done +112: [09:20:32] ------------------------------------- +112: [09:20:32] Test Github #3806: NaNs from AUTOCORR2D descriptor +112: [09:20:32] done + 96/235 Test #112: testAUTOCORR2D ......................... Passed 1.07 sec +test 116 + Start 116: testPBF + +116: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF +116: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +116: Test timeout computed to be: 1500 +69: Test +69: +69: AlexRxn.mrv 69: 69: Test 69: -69: ChiralTest.mrv +69: BadReactionSign.mrv 69: 69: Test 69: -69: SnCl2.mrv +69: bondArray_node.mrv 69: 69: Test 69: -69: SnH2Cl2.mrv +69: marvin03.mrv 69: 69: Test 69: -69: marvin01.mrv +69: marvin04.mrv 69: 69: Test 69: -69: marvin02.mrv +69: marvin08.mrv 69: 69: Test 69: -69: marvin07.mrv +69: marvin09.mrv 69: 69: Test 69: -69: marvin10.mrv +69: marvin11.mrv 69: 69: Test 69: -69: marvin06.mrv +69: marvin05.mrv 69: 69: Test 69: -69: marvin12.mrv +69: EmptyRxn.mrv 69: +69: [09:20:32] initialization failed +115: =>start test EEM +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 0 +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:20:32] Empty atom list: 'M ALS 1 0 F' on line 8. +116: [09:20:32] ------------------------------------- +116: [09:20:32] Basic PBF tests. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: de_DE.UTF-8 +70: [09:20:32] ------------------------------------- +70: [09:20:32] Test multithreading Locale Switching +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:20:32] Test multithreading (Done) +70: [09:20:32] ------------------------------------- +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [09:20:32] Explicit valence for atom # 3 Al, 6, is greater than permitted +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: *************************************** +70: *************************************** +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 69: Test 69: -69: EmptyMol.mrv +69: RxnNoCoords.mrv 69: 69: Test 69: -69: Sparse.mrv +69: mrvValenceZero.mrv 69: 69: Test 69: -69: Sparse2.mrv +69: condition_coordinates_mpoint.mrv 69: 69: Test 69: -69: Sparse3.mrv +69: marvin01.mrv 69: 69: Test 69: -69: MarvinNoCoords.mrv +69: aspirineSynthesisWithAttributes.mrv 69: 69: Test 69: -69: aspirin.mrv +69: marvin01.mrv 69: 69: Test 69: -69: MarvinStereoGroupsZeros.mrv +69: NewChiralTest 69: 69: Test 69: -69: MarvinStereoGroupsAbs.mrv +69: NewChiralTest 69: 69: Test 69: -69: triphenylphosphine.mrv +69: NewChiralTestNoChiral 69: 69: Test 69: -69: MarvinOldSuperGroupTest.mrv +69: NewChiralTestNoChiral 69: 69: Test 69: -69: RadicalTests.mrv +69: NewChiralTest2 69: 69: Test 69: -69: AnyBond.mrv +69: NewChiralTest2 69: 69: Test 69: -69: cisBenzene.mrv +69: NewChiralTest2AllChiral 69: 69: Test 69: -69: DativeBond.mrv +69: NewChiralTest2AllChiral 69: 69: Test 69: -69: MultipleSgroup.mrv +69: Vendor839 69: 69: Test 69: -69: SgroupExpanded.mrv +69: DoubleBondChain 69: 69: Test 69: -69: SgroupMultAttach.mrv +69: Na_Mg_Al_OH 69: 69: Test 69: -69: MarvinMissingX2.mrv +69: Pb 69: 69: Test 69: -69: MarvinMissingY2.mrv +69: O_Mg_Si 69: 69: Test 69: -69: DataSgroup.mrv +69: SquiggleBond 69: 69: Test 69: -69: MulticenterSgroup.mrv +69: BigMacrocycle +69: +69: Test 69: -69: [12:00:56] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[12:00:56] == testRemoveBadMatches -98: .[12:00:56] == testTimings -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test atom-pair fp generator -69: [12:00:56] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: Smiles1 +69: +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 100 +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 97/235 Test #69: testMrvToMol ........................... Passed 6.59 sec +test 117 + Start 117: testRDFcustom + +117: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom +117: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +117: Test timeout computed to be: 1500 +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:20:32] bond with order 0 found on line 7. This is not part of the MDL specification. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:20:32] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +70: [09:20:32] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +70: [09:20:32] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: generating smiles +70: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 +70: converting back +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: check isomorphism +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [09:20:32] Explicit valence for atom # 4 Al, 6, is greater than permitted +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [09:20:33] ------------------------------------- +114: [09:20:33] Test empty molecule BCUT. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 98/235 Test #114: testBCUT ............................... Passed 1.73 sec +test 118 + Start 118: testRDF + +118: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF +118: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +118: Test timeout computed to be: 1500 +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [09:20:33] Explicit valence for atom # 10 Si, 6, is greater than permitted +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 200 +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [09:20:33] done +116: [09:20:33] ------------------------------------- +116: [09:20:33] PBF edge cases. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [09:20:33] done + 99/235 Test #116: testPBF ................................ Passed 1.25 sec +test 119 + Start 119: testMORSE + +119: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE +119: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +119: Test timeout computed to be: 1500 +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +98: . +98: ---------------------------------------------------------------------- +98: Ran 11 tests in 3.751s +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 0.3211984634399414 seconds +98: Skipped 10000000 in 1.629040002822876 seconds +98: Skipped 10000000 in 0.4624922275543213 seconds +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +109: [09:20:33] +109: +109: **** +109: Invariant Violation +109: nonsense +109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +109: Failed Expression: token != tokens.end() +109: ---------- +109: Stacktrace: +109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 2# 0x00007FCF97E13DFD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 4# 0x00005622C6EAF183 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x00005622C6EAC731 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007FCF9702ED68 in /lib/x86_64-linux-gnu/libc.so.6 +109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +109: 8# 0x00005622C6EAC861 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: ---------- +109: **** +109: +109: [09:20:33] +109: +109: **** +109: Invariant Violation +109: nonsense no new line +109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +109: Failed Expression: token != tokens.end() +109: ---------- +109: Stacktrace: +109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 2# 0x00007FCF97E13DFD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 4# 0x00005622C6EAF183 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x00005622C6EAC731 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007FCF9702ED68 in /lib/x86_64-linux-gnu/libc.so.6 +109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +109: 8# 0x00005622C6EAC861 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: ---------- +109: **** +109: +109: [09:20:33] +109: +109: **** +109: Invariant Violation +109: nonsense with tab +109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +109: Failed Expression: token != tokens.end() +109: ---------- +109: Stacktrace: +109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 2# 0x00007FCF97E13DFD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 4# 0x00005622C6EAF183 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x00005622C6EAC731 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007FCF9702ED68 in /lib/x86_64-linux-gnu/libc.so.6 +109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +109: 8# 0x00005622C6EAC861 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: ---------- +109: **** +109: +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 300 +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +100/235 Test #109: testFragCatalog ........................ Passed 3.52 sec +test 120 + Start 120: test3D + +120: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D +120: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +120: Test timeout computed to be: 1500 +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +120: [09:20:33] ------------------------------------- +120: [09:20:33] Basic PMI tests. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +101/235 Test #98: pyChemReactionEnumerations ............. Passed 5.66 sec +test 121 + Start 121: testWHIM + +121: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM +121: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +121: Test timeout computed to be: 1500 +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +120: [09:20:34] done +120: [09:20:34] ------------------------------------- +120: [09:20:34] More PMI/NPR tests. +120: [09:20:34] done +120: [09:20:34] ------------------------------------- +120: [09:20:34] Basic NPR tests. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +120: [09:20:34] done +120: [09:20:34] ------------------------------------- +120: [09:20:34] PMI edge cases. +120: [09:20:34] done +120: [09:20:34] ------------------------------------- +120: [09:20:34] NPR edge cases. +120: [09:20:34] done +120: [09:20:34] ------------------------------------- +120: [09:20:34] 3D descriptors. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +120: [09:20:34] done +120: [09:20:34] ------------------------------------- +120: [09:20:34] 3D descriptor edge cases. +120: [09:20:34] done +120: [09:20:34] ------------------------------------- +120: [09:20:34] Inertial shape factor. +120: [09:20:34] done +102/235 Test #120: test3D ................................. Passed 0.62 sec +test 122 + Start 122: testGETAWAY + +122: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY +122: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +122: Test timeout computed to be: 1500 +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 400 +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [09:20:34] Explicit valence for atom # 2 O, 4, is greater than permitted +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [09:20:34] Explicit valence for atom # 3 Be, 4, is greater than permitted +89: [09:20:34] Explicit valence for atom # 3 Al, 6, is greater than permitted +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:20:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [09:20:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [09:20:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [09:20:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [09:20:34] deprecated group abbreviation ignored on line 24 +70: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +70: [09:20:34] +70: +70: **** +70: Post-condition Violation +70: Element 'Mv' not found +70: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +70: Failed Expression: anum > -1 +70: ---------- +70: Stacktrace: +70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +70: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 3# 0x00007F4963EC8391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 4# 0x00007F4963ED1CFA in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 5# 0x00007F4963ED207D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 9# 0x000055CEEDDE8CF5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 10# 0x000055CEEDE4F4F2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 11# 0x000055CEEDDCF9E3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 12# 0x00007F496342ED68 in /lib/x86_64-linux-gnu/libc.so.6 +70: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +70: 14# 0x000055CEEDDCFB11 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: ---------- +70: **** +70: +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +41: [09:20:34] done: 500000 +41: [09:20:34] Done +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: .............[09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +108: [09:20:34] SMILES Parse Error: syntax error while parsing: --- +108: [09:20:34] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:34] --- +108: [09:20:34] ^ +108: [09:20:34] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [09:20:34] dasfsadf +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [09:20:35] Explicit valence for atom # 27 P, 6, is greater than permitted +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +41: [09:20:35] Testing hanoi with a functor. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +41: [09:20:35] Done +41: [09:20:35] Testing basic partition refinement. +41: [09:20:35] Done +41: [09:20:35] Testing partition refinement with neighbors. +41: [09:20:35] Done +41: [09:20:35] testing canonicalization via tie breaking. +41: [09:20:35] Done +41: [09:20:35] testing canonicalization using the wrapper. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +41: [09:20:35] Done +41: [09:20:35] testing some specific ordering problems +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +41: [09:20:35] Finished +41: [09:20:35] testing chiral invariants. +41: [09:20:35] Finished +41: [09:20:35] testing unique ranks in w.r.t. renumbering. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: .[09:20:35] SMILES Parse Error: syntax error while parsing: mydoghasfleas +108: [09:20:35] SMILES Parse Error: check for mistakes around position 1: +108: [09:20:35] mydoghasfleas +108: [09:20:35] ^ +108: [09:20:35] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +41: [09:20:35] Finished +41: [09:20:35] testing mol fragments. +41: [09:20:35] Finished +41: [09:20:35] testing protein round-tripping. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +119: =>start test MORSE +119: =>read file +119: [09:20:35] test on : 365 molecules done +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103/235 Test #119: testMORSE .............................. Passed 2.10 sec +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 123 + Start 123: testAUTOCORR3D + +123: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D +123: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +123: Test timeout computed to be: 1500 +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [09:20:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: Elapsed time: 3.42547 s +115: Errors:0 +115: [09:20:35] test on : 500 molecules done +104/235 Test #115: testEEM ................................ Passed 3.58 sec +test 124 + Start 124: testCoulombMat + +124: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat +124: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +124: Test timeout computed to be: 1500 +124: ===================== Testing CoulombMat ======================= +124: CM test 1 mat Done +105/235 Test #124: testCoulombMat ......................... Passed 0.12 sec +test 125 + Start 125: descriptorsTestCatch + +125: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch +125: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +125: Test timeout computed to be: 1500 +70: [09:20:35] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +70: [09:20:35] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +125: Randomness seeded to: 3888679343 +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 +108: ....... +108: ---------------------------------------------------------------------- +108: Ran 21 tests in 4.514s +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 +125: Warning: Atom Count for residue GLU5A does not match expected count +70: ---------------------------------- +70: ---------------------------------- +70: [09:20:36] +70: +70: **** +70: Pre-condition Violation +70: rlabel out of range for MDL files +70: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp +70: Failed Expression: rlabel >= 0 && rlabel < 100 +70: ---------- +70: Stacktrace: +70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +70: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +70: 3# 0x000055CEEDDF60FF in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 4# 0x000055CEEDE4F56A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 5# 0x000055CEEDDCF9E3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 6# 0x00007F496342ED68 in /lib/x86_64-linux-gnu/libc.so.6 +70: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +70: 8# 0x000055CEEDDCFB11 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: ---------- +70: **** +70: +70: [09:20:36] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +121: =>start test WHIM +121: [09:20:36] test on : 365 molecules done +106/235 Test #121: testWHIM ............................... Passed 2.19 sec +test 126 + Start 126: pyMolDescriptors + +126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" +126: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap +126: Test timeout computed to be: 1500 +107/235 Test #108: pyFilterCatalog ........................ Passed 6.02 sec +test 127 + Start 127: pyMolDescriptors3D + +127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/test3D.py" +127: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap +127: Test timeout computed to be: 1500 +117: =>start test rdf custom +117: [09:20:37] test on : 365 molecules done +41: [09:20:37] Finished +41: [09:20:37] testing stability w.r.t. renumbering. +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: .[09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +126: ..[09:20:37] +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-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +126: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +126: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitDescriptors.so.1 +126: 3# 0x00007F07D87169C2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 4# 0x00007F07D8726E16 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +126: 6# 0x00007F07DC80866C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +126: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +126: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +126: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/obj-x86_64-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-202409.6/obj-x86_64-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-202409.6/obj-x86_64-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-202409.6/obj-x86_64-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-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +126: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +126: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 17# 0x00007F07DA3B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 18# 0x00007F07DA3B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 19# 0x00007F07DA3B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 20# 0x00007F07DA3B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 21# 0x00007F07DA3B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +126: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +126: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +126: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +126: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +126: 27# 0x00007F07DC805406 in /lib/x86_64-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# 0x00000000005BEE79 in /usr/bin/python3 +126: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 32# 0x0000000000547080 in /usr/bin/python3 +126: 33# 0x00000000006AB720 in /usr/bin/python3 +126: 34# _PyObject_MakeTpCall in /usr/bin/python3 +126: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 36# 0x00000000005BEE79 in /usr/bin/python3 +126: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 38# 0x0000000000547080 in /usr/bin/python3 +126: 39# 0x00000000006AB720 in /usr/bin/python3 +126: 40# _PyObject_MakeTpCall in /usr/bin/python3 +126: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 42# 0x00000000005BEE79 in /usr/bin/python3 +126: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 44# 0x0000000000547080 in /usr/bin/python3 +126: 45# 0x00000000006AB720 in /usr/bin/python3 +126: 46# _PyObject_MakeTpCall in /usr/bin/python3 +126: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +126: 48# 0x000000000059582E 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# 0x000000000066A861 in /usr/bin/python3 +126: 53# 0x000000000066670C in /usr/bin/python3 +126: 54# 0x000000000067F713 in /usr/bin/python3 +126: 55# 0x000000000067ECE3 in /usr/bin/python3 +126: 56# 0x000000000067EB1E in /usr/bin/python3 +126: 57# Py_RunMain in /usr/bin/python3 +126: 58# Py_BytesMain in /usr/bin/python3 +126: 59# 0x00007F07DD0DED68 in /lib/x86_64-linux-gnu/libc.so.6 +126: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +126: 61# _start in /usr/bin/python3 +126: ---------- +126: **** +126: +123: =>start test autocorr3D +123: [09:20:37] test on : 365 molecules done +108/235 Test #123: testAUTOCORR3D ......................... Passed 1.94 sec +test 128 + Start 128: testFingerprints + +128: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints +128: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +128: Test timeout computed to be: 1500 +126: ...Warning: Atom Count for residue GLU5A does not match expected count +126: Warning: Atom Count for residue ASN39A does not match expected count +126: Warning: Atom Count for residue GLU53A does not match expected count +126: Warning: Atom Count for residue ARG64A does not match expected count +126: Warning: Atom Count for residue LYS80A does not match expected count +126: Warning: Atom Count for residue GLU150A does not match expected count +126: Warning: Atom Count for residue ASN157A does not match expected count 128: 128: 128: @@ -23191,7 +25241,6 @@ 128: 128: 128: ------------------- -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: 128: 128: @@ -23237,10 +25286,6 @@ 128: 128: 128: ------------------- -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: SMI: Oc1cc2[nH]cnc2c(O)n1 128: Atoms: 128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 @@ -23401,11 +25446,6 @@ 128: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 9 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -36: [12:00:56] Maximum BFS search size exceeded. -36: This is likely due to a highly symmetric fused ring system. -97: ...[12:00:56] -97: -97: **** 128: 10 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: Bonds: 128: 0 0->1 order: a conj?: 1 aromatic?: 1 @@ -23436,7 +25476,6 @@ 128: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 1 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: 3 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 128: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 5 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 @@ -23545,30 +25584,13 @@ 128: 128: SMI: c1(O)c2c(cc(O)n1)[nH]cn2 128: Atoms: -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test atom-pair fp generator with different arguments -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -130: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -130: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -130: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator 128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -130: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator 128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -129: [12:00:56] done -129: [12:00:56] ------------------------------------- -129: [12:00:56] Test MHFP shingling creation -130: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator 128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -130: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator 128: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 128: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -130: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator 128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 8 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 128: 9 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 @@ -23580,96 +25602,6 @@ 128: 3 3->4 order: a conj?: 1 aromatic?: 1 128: 4 4->5 order: a conj?: 1 aromatic?: 1 128: 5 5->6 order: 1 conj?: 1 -97: Pre-condition Violation -97: getNumImplicitHs() called without preceding call to calcImplicitValence() -97: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp -97: Failed Expression: d_implicitValence > -1 -97: ---------- -97: Stacktrace: -97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 25# 0x00007FEA58B8366C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so -97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x00007FEA567B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x00007FEA567B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x00007FEA567B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x00007FEA567B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x00007FEA567B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 46# 0x00007FEA58B80406 in /lib/x86_64-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# 0x00000000005BEE79 in /usr/bin/python3 -97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 51# 0x0000000000547080 in /usr/bin/python3 -97: 52# 0x00000000006AB720 in /usr/bin/python3 -97: 53# _PyObject_MakeTpCall in /usr/bin/python3 -97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 55# 0x00000000005BEE79 in /usr/bin/python3 -97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 57# 0x0000000000547080 in /usr/bin/python3 -97: 58# 0x00000000006AB720 in /usr/bin/python3 -97: 59# _PyObject_MakeTpCall in /usr/bin/python3 -97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 61# 0x00000000005BEE79 in /usr/bin/python3 -97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 63# 0x0000000000547080 in /usr/bin/python3 -97: 64# 0x00000000006AB720 in /usr/bin/python3 -97: 65# _PyObject_MakeTpCall in /usr/bin/python3 -97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 67# 0x0000000000595987 in /usr/bin/python3 -97: 68# _PyObject_MakeTpCall in /usr/bin/python3 -97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 70# PyEval_EvalCode in /usr/bin/python3 -97: 71# 0x000000000066A861 in /usr/bin/python3 -97: 72# 0x000000000066670C in /usr/bin/python3 -97: 73# 0x000000000067F713 in /usr/bin/python3 -97: 74# 0x000000000067ECE3 in /usr/bin/python3 -97: 75# 0x000000000067EB1E in /usr/bin/python3 -97: 76# Py_RunMain in /usr/bin/python3 -97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x00007FEA59587D68 in /lib/x86_64-linux-gnu/libc.so.6 -97: 79# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -97: 80# _start in /usr/bin/python3 -97: ---------- -97: **** -97: 128: 6 5->7 order: a conj?: 1 aromatic?: 1 128: 7 3->8 order: a conj?: 1 aromatic?: 1 128: 8 8->9 order: a conj?: 1 aromatic?: 1 @@ -23782,852 +25714,589 @@ 128: 128: ------------------- 128: -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [12:00:56] -97: -97: **** -131: Randomness seeded to: 526407885 +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Morgan Fingerprints. +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Morgan Fingerprints using fromAtoms argument. +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Morgan Fingerprints as bit vects. +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Morgan Fingerprints with feature invariants. +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test additional Morgan fingerprints options. +41: [09:20:37] Finished +41: [09:20:37] testing smiles round-tripping. +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Atom Codes. +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Atom Pairs. +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Atom Pairs part 2. +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Topological Torsions. +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Bulk Topological Torsions. +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +125: Warning: Atom Count for residue ASN39A does not match expected count +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +70: [09:20:37] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +70: [09:20:37] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: Warning: Atom Count for residue GLU5A does not match expected count +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Hashed Atom Pairs. +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Hashed torsions. +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Rooted Atom Pairs. +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test ignoring atoms in Atom Pairs. +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Rooted Topological Torsions. +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test ignoring atoms in Topological Torsions. +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test atom info from morgan fingerprints. +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test atom info from morgan fingerprints including Info Redundant Environments. +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] ------------------------------------- +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] ------------------------------------- +128: [09:20:37] ------------------------------------- +128: [09:20:37] ------------------------------------- +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Atom Pairs including info about chirality. +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test Topological Torsions including info about chirality. +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test GitHub Issue 25: fingerprint backwards compatibility. +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test GitHub Issue 151: PatternFingerprint problems +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test 3D atom pairs. +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +128: [09:20:37] done +128: [09:20:37] ------------------------------------- +128: [09:20:37] Test multithreading with the pattern FP +128: reading molecules +89: [09:20:37] Explicit valence for atom # 9 N, 6, is greater than permitted +128: pass 1 +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +127: ........ +127: ---------------------------------------------------------------------- +127: Ran 8 tests in 0.620s +127: +127: OK +70: [09:20:37] Empty atom list: 'M ALS 1 0 F' on line 8. +29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +109/235 Test #70: fileParsersTest1 ....................... Passed 12.07 sec +test 129 + Start 129: testMHFPFingerprint + +129: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint +129: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +129: Test timeout computed to be: 1500 +129: [09:20:38] ------------------------------------- +129: [09:20:38] Test MHFP fingerprint encoder initialization +129: [09:20:38] done +129: [09:20:38] ------------------------------------- +129: [09:20:38] Test MHFP shingling creation +41: [09:20:38] Finished +41: [09:20:38] testing github #1567: Non-canonical result from MolFragmentToSmiles() +41: [09:20:38] Finished +110/235 Test #41: hanoiTest .............................. Passed 13.36 sec +test 130 + Start 130: testFingerprintGenerators + +130: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators +130: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +130: Test timeout computed to be: 1500 +128: pass 2 +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +111/235 Test #127: pyMolDescriptors3D ..................... Passed 1.94 sec +test 131 + Start 131: fpTestCatch + +131: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch +131: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +131: Test timeout computed to be: 1500 +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test atom-pair fp generator +129: [09:20:38] done +129: [09:20:38] ------------------------------------- +129: [09:20:38] Test MHFP hashing of string and uint arrays +129: [09:20:38] done +129: [09:20:38] ------------------------------------- +129: [09:20:38] Test SECFP fingerprint functionality +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test atom-pair fp generator with different arguments +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +130: [09:20:38] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:20:38] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:20:38] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:20:38] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:20:38] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:20:38] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:20:38] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:20:38] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:20:38] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:20:38] DEPRECATION WARNING: please use AtomPairGenerator +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test atom-pair additional output +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test Folded Atom Pairs. +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test Rooted Atom Pairs. +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test ignoring atoms in Atom Pairs. +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test Atom Pairs including info about chirality. +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test Morgan Fingerprints. +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test morgan fp generator +131: Randomness seeded to: 893304293 131: =============================================================================== 131: All tests passed (188 assertions in 16 test cases) 131: -130: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator - 91/235 Test #131: fpTestCatch ............................ Passed 0.09 sec +112/235 Test #131: fpTestCatch ............................ Passed 0.11 sec +test 132 + Start 132: fpGenTestCatch + +132: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch +132: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +132: Test timeout computed to be: 1500 +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test Morgan Fingerprints using fromAtoms argument. +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test Morgan Fingerprints as bit vects. +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test Morgan Fingerprints with feature invariants. +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test additional Morgan fingerprints options. +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Single atoms setting radius 1 bits in Morgan fingerprints +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test different invariant generator combinations +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test invariant overriding +130: [09:20:38] done +130: [09:20:38] ------------------------------------- +130: [09:20:38] Test RDKit fp generator +129: [09:20:38] done +113/235 Test #129: testMHFPFingerprint .................... Passed 0.37 sec test 133 Start 133: pyTestGenerator 133: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 133: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 133: Test timeout computed to be: 1500 -69: Test -69: -69: GenericSgroup.mrv -69: -69: Test -69: -69: MonomerSgroup.mrv -69: -69: Test -69: -69: modification_sgroup.mrv -69: -69: Test -69: -69: copolymer_sgroup.mrv -69: -69: Test -69: -69: MultipleSgroupParentInMiddleOfAtomBlock.mrv -69: -69: Test -69: -69: EmbeddedSgroups.mrv -69: -69: Test -69: -69: marvin03.mrv -69: -69: Test -69: -69: MarvinBadMissingMolID.mrv -69: -69: [12:00:56] -69: -69: **** -69: Test Assert -69: Expression Failed: -69: Violation occurred on line 329 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp -69: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# 0x000056050F77699F in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -69: 3# 0x000056050F78169C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -69: 4# 0x000056050F76EA5D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -69: 5# 0x00007F3491C33D68 in /lib/x86_64-linux-gnu/libc.so.6 -69: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -69: 7# 0x000056050F76EBE1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -69: ---------- -69: **** -69: -69: Test -69: -69: MarvinBadMissingAtomID.mrv -69: -69: Expected id, elementType for an atom definition in MRV file -69: Test -69: -69: MarvinBadX2.mrv -69: -69: The values x2 and y2 must be large floats in MRV file -69: Test -69: -69: MarvinBadY2.mrv -69: -69: The values x2 and y2 must be large floats in MRV file -69: Test -69: -69: MarvinBadStereoGroupsAbs.mrv -69: -69: Unrecognized group definition -97: Pre-condition Violation -97: getNumImplicitHs() called without preceding call to calcImplicitValence() -97: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp -97: Failed Expression: d_implicitValence > -1 -97: ---------- -97: Stacktrace: -97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 25# 0x00007FEA58B8366C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so -97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x00007FEA567B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x00007FEA567B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x00007FEA567B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x00007FEA567B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x00007FEA567B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -97: 46# 0x00007FEA58B80406 in /lib/x86_64-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# 0x00000000005BEE79 in /usr/bin/python3 -97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 51# 0x0000000000547080 in /usr/bin/python3 -97: 52# 0x00000000006AB720 in /usr/bin/python3 -97: 53# _PyObject_MakeTpCall in /usr/bin/python3 -97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 55# 0x00000000005BEE79 in /usr/bin/python3 -97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 57# 0x0000000000547080 in /usr/bin/python3 -97: 58# 0x00000000006AB720 in /usr/bin/python3 -97: 59# _PyObject_MakeTpCall in /usr/bin/python3 -97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 61# 0x00000000005BEE79 in /usr/bin/python3 -97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 63# 0x0000000000547080 in /usr/bin/python3 -97: 64# 0x00000000006AB720 in /usr/bin/python3 -97: 65# _PyObject_MakeTpCall in /usr/bin/python3 -97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 67# 0x0000000000595987 in /usr/bin/python3 -97: 68# _PyObject_MakeTpCall in /usr/bin/python3 -97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 70# PyEval_EvalCode in /usr/bin/python3 -97: 71# 0x000000000066A861 in /usr/bin/python3 -97: 72# 0x000000000066670C in /usr/bin/python3 -97: 73# 0x000000000067F713 in /usr/bin/python3 -97: 74# 0x000000000067ECE3 in /usr/bin/python3 -97: 75# 0x000000000067EB1E in /usr/bin/python3 -97: 76# Py_RunMain in /usr/bin/python3 -97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x00007FEA59587D68 in /lib/x86_64-linux-gnu/libc.so.6 -97: 79# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -97: 80# _start in /usr/bin/python3 -97: ---------- -97: **** -97: -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -69: Test -69: -69: MarvinBadElementType.mrv -69: -69: Test -69: -69: MarvinBadMissingBondID.mrv -69: -69: Test -69: -69: MarvinBadMissingBondAtomRefs -69: -69: Test -69: -69: MarvinBadMissingBondOrder.mrv -69: -69: bond must have one of: order, queryType, or convention in MRV File -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Morgan Fingerprints. -69: Test -69: -69: MarvinBadMissingSruMolID.mrv -69: -69: Expected a molID in MRV file -69: Test -69: -69: MarvinBadMissingSruID.mrv -69: -69: Test -69: -69: MarvinBadMissingSruRole.mrv -69: -69: Test -69: -69: MarvinBadMissingSruAtomRef.mrv -69: -69: Test -69: -69: MarvinBadMissingSruTitle.mrv -69: -69: Test -69: -69: MarvinBadSruAtomRef.mrv -69: -69: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -103: ..... -103: ---------------------------------------------------------------------- -103: Ran 5 tests in 0.102s -103: -103: OK -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: Test -69: -69: MarvinBadSruID.mrv -69: -69: Test -69: -69: MarvinBadSruRole.mrv -69: -69: Test -69: -69: MarvinBadSruAtomRef.mrv -69: -69: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: Test -69: -69: MarvinBadSruAtomRef.mrv -69: -69: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Morgan Fingerprints using fromAtoms argument. -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Morgan Fingerprints as bit vects. -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Morgan Fingerprints with feature invariants. -69: Test -69: -69: MarvinBadSruConnect.mrv -69: -69: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test additional Morgan fingerprints options. -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Atom Codes. -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Atom Pairs. -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Atom Pairs part 2. -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Topological Torsions. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Bulk Topological Torsions. -97: .........[12:00:56] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [12:00:56] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [12:00:56] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [12:00:56] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -130: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test atom-pair additional output -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test Folded Atom Pairs. -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test Rooted Atom Pairs. -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test ignoring atoms in Atom Pairs. -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test Atom Pairs including info about chirality. -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test Morgan Fingerprints. -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test morgan fp generator -97: .[12:00:56] product atom-mapping number 1 found multiple times. -97: [12:00:56] product atom-mapping number 1 found multiple times. -129: [12:00:56] done -129: [12:00:56] ------------------------------------- -129: [12:00:56] Test MHFP hashing of string and uint arrays -129: [12:00:56] done -129: [12:00:56] ------------------------------------- -129: [12:00:56] Test SECFP fingerprint functionality -69: Test -69: -69: MarvinBadSupAttachAtom.mrv -69: -69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -69: Test -69: -69: MarvinBadSupAttachBond.mrv -69: -69: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -69: Test -69: -69: MarvinBadSupAttachOrder.mrv -69: -69: Order for an AttachmentPoint definition must be an integer in MRV file -69: Test -69: -69: MarvinBadSupAttachAtom.mrv -69: -69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -69: Test -69: -69: MarvinBadSupAttachAtom.mrv -69: -69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -69: Test -69: -69: MarvinBadSupAttachAtom.mrv -69: -69: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -97: ................[12:00:56] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: [12:00:56] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -69: Test -69: -69: MarvinBadSupMissingAttachBond.mrv -69: -69: No attachment point found for bond to the condensed atom in a superatomSgroup -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -97: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -69: Test -69: -69: MarvinBadSupMissingAttachOrder.mrv -69: -69: Expected atom, order and bond, for an AttachmentPoint definition in MRV file -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [12:00:56] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -129: [12:00:56] done -97: ..[12:00:56] reactant 2 has no mapped atoms. -97: [12:00:56] reactant 2 has no mapped atoms. -97: [12:00:56] product 1 has no mapped atoms. - 92/235 Test #129: testMHFPFingerprint .................... Passed 0.18 sec +125: Warning: Atom Count for residue GLU53A does not match expected count +132: Randomness seeded to: 2962814758 +132: =============================================================================== +132: All tests passed (2737 assertions in 7 test cases) +132: +114/235 Test #132: fpGenTestCatch ......................... Passed 0.45 sec test 134 Start 134: pyTestMHFP 134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 134: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 134: Test timeout computed to be: 1500 -125: Randomness seeded to: 3876931346 -125: Warning: Atom Count for residue GLU5A does not match expected count -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test Morgan Fingerprints using fromAtoms argument. -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test Morgan Fingerprints as bit vects. -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test Morgan Fingerprints with feature invariants. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -97: ........[12:00:56] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -97: [12:00:56] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -97: [12:00:56] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -97: [12:00:56] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -97: .[12:00:56] reactant atom-mapping number 1 found multiple times. -97: [12:00:56] product atom-mapping number 2 not found in reactants. -125: Warning: Atom Count for residue ASN39A does not match expected count -97: [12:00:56] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 4 -97: [12:00:56] product atom-mapping number 5 not found in reactants. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -125: Warning: Atom Count for residue GLU53A does not match expected count -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test additional Morgan fingerprints options. -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Single atoms setting radius 1 bits in Morgan fingerprints -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test different invariant generator combinations -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test invariant overriding -130: [12:00:56] done -130: [12:00:56] ------------------------------------- -130: [12:00:56] Test RDKit fp generator -125: Warning: Atom Count for residue ARG64A does not match expected count -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -125: Warning: Atom Count for residue LYS80A does not match expected count -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -125: Warning: Atom Count for residue GLU150A does not match expected count -125: Warning: Atom Count for residue ASN157A does not match expected count -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -110: ......... -110: ---------------------------------------------------------------------- -110: Ran 9 tests in 0.157s -110: -110: OK -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -89: [12:00:56] Explicit valence for atom # 9 N, 6, is greater than permitted -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator - 93/235 Test #103: pyTautomerQuery ........................ Passed 0.97 sec +89: [09:20:38] Explicit valence for atom # 3 Al, 6, is greater than permitted +126: Warning: Atom Count for residue ASN39A does not match expected count +130: [09:20:39] done +130: [09:20:39] ------------------------------------- +130: [09:20:39] Test unfolded version of RDKFP +130: [09:20:39] ------------------------------------- +130: [09:20:39] Test topological torsion fp generator +130: [09:20:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:20:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:20:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:20:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:20:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:20:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:20:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:20:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:20:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +29: All 191 tests passed +130: [09:20:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [09:20:39] done +130: [09:20:39] ------------------------------------- +130: [09:20:39] Test Topological Torsions. +130: [09:20:39] done +130: [09:20:39] ------------------------------------- +130: [09:20:39] Test Folded torsions. +130: [09:20:39] done +130: [09:20:39] ------------------------------------- +130: [09:20:39] Test Bulk Topological Torsions. +89: [09:20:39] Explicit valence for atom # 4 Al, 6, is greater than permitted +118: =>start test rdf +118: [09:20:39] test on : 365 molecules done +115/235 Test #118: testRDF ................................ Passed 6.30 sec test 135 Start 135: testPartialCharges 135: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 135: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges 135: Test timeout computed to be: 1500 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: ........./build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> -97: png = open(fname, 'rb').read() -97: ResourceWarning: Enable tracemalloc to get the object allocation traceback -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -97: [12:00:56] Found a SCD/SED line with missing/empty SDT specification at line 34 -97: [12:00:56] Found a SCD/SED line with missing/empty SDT specification at line 36 -97: [12:00:56] Found a SCD/SED line with missing/empty SDT specification at line 38 -97: [12:00:56] Found a SCD/SED line with missing/empty SDT specification at line 40 -97: [12:00:56] Found a SCD/SED line with missing/empty SDT specification at line 42 -97: [12:00:56] Found a SCD/SED line with missing/empty SDT specification at line 87 -97: [12:00:56] Found a SCD/SED line with missing/empty SDT specification at line 89 -97: [12:00:56] Found a SCD/SED line with missing/empty SDT specification at line 91 -97: [12:00:56] Found a SCD/SED line with missing/empty SDT specification at line 93 -97: [12:00:56] Found a SCD/SED line with missing/empty SDT specification at line 95 -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -132: Randomness seeded to: 962838260 -132: =============================================================================== -132: All tests passed (2737 assertions in 7 test cases) -132: -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -114: [12:00:56] ------------------------------------- -114: [12:00:56] Test empty molecule BCUT. - 94/235 Test #114: testBCUT ............................... Passed 0.80 sec +125: Warning: Atom Count for residue ARG64A does not match expected count +116/235 Test #135: testPartialCharges ..................... Passed 0.06 sec test 136 Start 136: pyPartialCharges 136: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 136: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 136: Test timeout computed to be: 1500 -97: ..[12:00:56] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [12:00:56] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 95/235 Test #132: fpGenTestCatch ......................... Passed 0.25 sec +89: [09:20:39] Explicit valence for atom # 10 Si, 6, is greater than permitted +117/235 Test #43: resMolSupplierTest ..................... Passed 14.79 sec test 137 Start 137: testMolTransforms 137: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 137: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms 137: Test timeout computed to be: 1500 -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [12:00:56] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [12:00:56] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [12:00:56] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [12:00:56] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [12:00:56] reaction has no reactants -97: [12:00:56] reaction has no products -97: [12:00:56] initialization failed -97: [12:00:56] reaction has no reactants -97: [12:00:56] reaction has no products -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator - 96/235 Test #135: testPartialCharges ..................... Passed 0.07 sec -test 138 - Start 138: molTransformsTestCatch - -138: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch -138: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms -138: Test timeout computed to be: 1500 -68: ..............[12:00:56] SMILES Parse Error: syntax error while parsing: invalidsmiles -68: [12:00:56] SMILES Parse Error: check for mistakes around position 1: -68: [12:00:56] invalidsmiles -68: [12:00:56] ^ -68: [12:00:56] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 200 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -93: [12:00:56] reactant 0 has no mapped atoms. -93: [12:00:56] product 0 has no mapped atoms. -93: [12:00:56] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -97: .[12:00:56] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [12:00:56] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -97: [12:00:56] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [12:00:56] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -92: Randomness seeded to: 4190628387 -92: =============================================================================== -92: All tests passed (11480 assertions in 38 test cases) -92: -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator - 97/235 Test #92: testGenericGroups ...................... Passed 1.14 sec -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -test 139 - Start 139: pyMolTransforms - -139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" -139: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap -139: Test timeout computed to be: 1500 -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -97: [12:00:56] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [12:00:56] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [12:00:56] reaction has no reactants -97: [12:00:56] reaction has no products -97: [12:00:56] initialization failed -97: [12:00:56] reaction has no reactants -97: [12:00:56] reaction has no products -97: . -97: ---------------------------------------------------------------------- -97: Ran 54 tests in 0.300s -97: -97: OK -97: ******************************************** -97: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -97: -69: Test -69: -69: marvin03.mrv -69: -69: Test -69: -69: Cubane.mrv -69: -69: Test -69: -69: FalseAtropisomer.mrv -69: -69: Test -69: -69: AtropEnhancedStereo.mrv -69: -69: Test -69: -69: AtropManyChirals.mrv -69: -69: Test -69: -69: AtropManyChiralsEnhanced.mrv -69: -69: Test -69: -69: AtropManyChiralsEnhanced2.mrv -69: -69: Test -69: -69: AtropManyChiralsEnhanced3.mrv -69: -69: Test -69: -69: AtropManyChiralsEnhanced4.mrv -69: -69: Test -69: -69: BMS-986142_3d_chiral.mrv -69: -69: Test -69: -69: BMS-986142_3d.mrv -69: -69: Test -69: -69: BMS-986142_atrop1.mrv -69: -69: Test -69: -69: BMS-986142_atrop2.mrv -69: -69: Test -69: -69: BMS-986142_atrop3.mrv -69: -69: Test -69: -69: BMS-986142_atrop4.mrv -69: -69: Test -69: -69: BMS-986142_atrop5.mrv -69: -69: [12:00:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [12:00:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored - 98/235 Test #110: pyFragCatalog .......................... Passed 0.98 sec -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 140 - Start 140: forceFieldHelpersCatch - -140: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch -140: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers -140: Test timeout computed to be: 1500 - 99/235 Test #93: testReaction ........................... Passed 1.14 sec -test 141 - Start 141: testMMFFForceFieldHelpers - -141: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers -141: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF -141: Test timeout computed to be: 1500 -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -120: [12:00:56] done -120: [12:00:56] ------------------------------------- -120: [12:00:56] More PMI/NPR tests. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -120: [12:00:56] done -120: [12:00:56] ------------------------------------- -120: [12:00:56] Basic NPR tests. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -125: Warning: Atom Count for residue GLU5A does not match expected count -69: Test -69: -69: BMS-986142_atrop6.mrv -69: -69: Test -69: -69: BMS-986142_atrop7.mrv -69: -69: Test -69: -69: BMS-986142_atrop8.mrv -69: -69: [12:00:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [12:00:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +133: .............. +133: ---------------------------------------------------------------------- +133: Ran 14 tests in 0.434s +133: +133: OK 137: *********************************************************** 137: Testing MolTransforms 137: --------------------------------- @@ -24658,421 +26327,153 @@ 137: testWeightedCentroid 137: 137: *********************************************************** -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -100/235 Test #137: testMolTransforms ...................... Passed 0.11 sec +118/235 Test #137: testMolTransforms ...................... Passed 0.16 sec +test 138 + Start 138: molTransformsTestCatch + +138: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch +138: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms +138: Test timeout computed to be: 1500 +130: [09:20:39] done +130: [09:20:39] ------------------------------------- +130: [09:20:39] Test Rooted Topological Torsions. +130: [09:20:39] done +130: [09:20:39] ------------------------------------- +130: [09:20:39] Test ignoring atoms in Topological Torsions. +130: [09:20:39] done +130: [09:20:39] ------------------------------------- +130: [09:20:39] ------------------------------------- +130: [09:20:39] Test Topological Torsions including info about chirality. +130: [09:20:39] done +130: [09:20:39] ------------------------------------- +130: [09:20:39] Test GitHub Issue 25: fingerprint backwards compatibility. +130: [09:20:39] done +130: [09:20:39] ------------------------------------- +130: [09:20:39] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +130: [09:20:39] done +130: [09:20:39] ------------------------------------- +130: [09:20:39] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +138: Randomness seeded to: 666995503 +138: =============================================================================== +138: All tests passed (4 assertions in 1 test case) +138: +130: [09:20:39] done +130: [09:20:39] ------------------------------------- +130: [09:20:39] Test convenience and bulk fp calculation functions +119/235 Test #138: molTransformsTestCatch ................. Passed 0.05 sec +test 139 + Start 139: pyMolTransforms + +139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" +139: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap +139: Test timeout computed to be: 1500 +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +120/235 Test #133: pyTestGenerator ........................ Passed 1.82 sec +test 140 + Start 140: forceFieldHelpersCatch + +140: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch +140: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers +140: Test timeout computed to be: 1500 +140: Randomness seeded to: 3009917865 +140: =============================================================================== +140: All tests passed (17 assertions in 2 test cases) +140: +121/235 Test #140: forceFieldHelpersCatch ................. Passed 0.11 sec +test 141 + Start 141: testMMFFForceFieldHelpers + +141: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers +141: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF +141: Test timeout computed to be: 1500 +141: [09:20:40] ------------------------------------- +141: [09:20:40] Test MMFF atom types. +141: [09:20:40] done +141: [09:20:40] ------------------------------------- +141: [09:20:40] Testing MMFF builder tools. +141: [09:20:40] done +141: [09:20:40] ------------------------------------- +141: [09:20:40] Testing MMFF builder+minimization. +141: [09:20:40] done +141: [09:20:40] ------------------------------------- +141: [09:20:40] Testing Issue239. +141: [09:20:40] done +141: [09:20:40] ------------------------------------- +141: [09:20:40] Testing calcEnergy with passed coords. +117: =>start test morse custom +117: [09:20:40] test on : 365 molecules done +136: ....... +136: ---------------------------------------------------------------------- +136: Ran 7 tests in 0.494s +136: +136: OK +141: [09:20:40] done +141: [09:20:40] ------------------------------------- +141: [09:20:40] Testing calcGrad. +125: Warning: Atom Count for residue LYS80A does not match expected count +134: .. +134: ---------------------------------------------------------------------- +126: Warning: Atom Count for residue GLU53A does not match expected count +134: Ran 2 tests in 0.353s +134: +134: OK +141: [09:20:40] done +141: [09:20:40] ------------------------------------- +141: [09:20:40] Testing Issue242. +89: [09:20:41] Explicit valence for atom # 2 O, 4, is greater than permitted +139: ........ +139: ---------------------------------------------------------------------- +139: Ran 8 tests in 0.142s +139: +139: OK +89: [09:20:41] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [09:20:41] Explicit valence for atom # 3 Be, 4, is greater than permitted +141: [09:20:41] done +141: [09:20:41] ------------------------------------- +141: [09:20:41] Testing github 308: crash during MMFF parameterization . +141: [09:20:41] ------------------------------------- +141: [09:20:41] Testing SFIssue1653802. +141: [09:20:41] done +141: [09:20:41] ------------------------------------- +141: [09:20:41] Testing SFIssue2378119. +141: [09:20:41] done +141: [09:20:41] ------------------------------------- +141: [09:20:41] Test MMFF force-field parameter getters. +141: [09:20:41] ------------------------------------- +141: [09:20:41] Test MMFF multithreading +122/235 Test #136: pyPartialCharges ....................... Passed 1.74 sec test 142 Start 142: testMMFFForceFieldHelpersMultiThread 142: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 142: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 142: Test timeout computed to be: 1500 -138: Randomness seeded to: 2944723651 -138: =============================================================================== -138: All tests passed (4 assertions in 1 test case) -138: -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -101/235 Test #138: molTransformsTestCatch ................. Passed 0.09 sec +141: generating reference data +123/235 Test #139: pyMolTransforms ........................ Passed 1.31 sec test 143 Start 143: testUFFForceFieldHelpers 143: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers 143: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF 143: Test timeout computed to be: 1500 -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -141: [12:00:56] ------------------------------------- -141: [12:00:56] Test MMFF atom types. -69: Test -69: -69: BMS-986142_atropBad2.mrv -69: -69: [12:00:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -140: Randomness seeded to: 267816662 -140: =============================================================================== -140: All tests passed (17 assertions in 2 test cases) -140: -89: [12:00:56] Explicit valence for atom # 3 Al, 6, is greater than permitted -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -102/235 Test #140: forceFieldHelpersCatch ................. Passed 0.08 sec -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -test 144 - Start 144: testCrystalForceField - -144: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField -144: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF -144: Test timeout computed to be: 1500 -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -141: [12:00:56] done -141: [12:00:56] ------------------------------------- -141: [12:00:56] Testing MMFF builder tools. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] done -142: [12:00:56] ------------------------------------- -142: [12:00:56] Test MMFF multithreading -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Hashed Atom Pairs. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Hashed torsions. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Rooted Atom Pairs. -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test ignoring atoms in Atom Pairs. -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Rooted Topological Torsions. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test ignoring atoms in Topological Torsions. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test atom info from morgan fingerprints. -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test atom info from morgan fingerprints including Info Redundant Environments. -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] ------------------------------------- -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -144: ------------------------------------- -144: Test CrystalFF torsional term. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] ------------------------------------- -143: [12:00:56] ------------------------------------- -143: [12:00:56] Test UFF atom labels. -141: [12:00:56] done -141: [12:00:56] ------------------------------------- -141: [12:00:56] Testing MMFF builder+minimization. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] ------------------------------------- -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] ------------------------------------- -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Atom Pairs including info about chirality. -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test Topological Torsions including info about chirality. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test GitHub Issue 25: fingerprint backwards compatibility. -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test GitHub Issue 151: PatternFingerprint problems -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [12:00:56] done -143: [12:00:56] ------------------------------------- -143: [12:00:56] Test UFF atom typer. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: Test -69: -69: JDQ443_3d.mrv -69: -69: Test -69: -69: JDQ443_atrop1.mrv -69: -69: Test -69: -69: JDQ443_atrop2.mrv -69: -69: Test -69: -69: JDQ443_atrop3.mrv -69: -69: Test -69: -69: JDQ443_atropBad1.mrv -69: -69: [12:00:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -143: [12:00:56] done -143: [12:00:56] ------------------------------------- -143: [12:00:56] Testing UFF builder tools. -143: [12:00:56] done -143: [12:00:56] ------------------------------------- -143: [12:00:56] Testing UFF builder+minimization. -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test 3D atom pairs. -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -128: [12:00:56] done -128: [12:00:56] ------------------------------------- -128: [12:00:56] Test multithreading with the pattern FP -128: reading molecules -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103/235 Test #97: pyChemReactions ........................ Passed 1.28 sec -test 145 - Start 145: pyForceFieldHelpers - -145: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" -145: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap -145: Test timeout computed to be: 1500 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [12:00:56] Explicit valence for atom # 4 Al, 6, is greater than permitted -69: Test -69: -69: RP-6306_atrop1.mrv -69: -69: Test -69: -69: RP-6306_atrop2.mrv -69: -69: Test -69: -69: RP-6306_atrop3.mrv -69: -69: Test -69: -69: RP-6306_atrop4.mrv -69: -69: Test -69: -69: RP-6306_atrop5.mrv -69: -69: [12:00:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [12:00:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: Test -69: -69: RP-6306_atropBad1.mrv -69: -69: [12:00:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -69: Test -69: -69: RP-6306_atropBad2.mrv -69: -69: [12:00:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [12:00:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [12:00:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [12:00:56] done -141: [12:00:56] ------------------------------------- -141: [12:00:56] Testing Issue239. -128: pass 1 -128: launch :0 -128: launch :1 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: launch :2 -128: launch :3 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [12:00:56] Explicit valence for atom # 10 Si, 6, is greater than permitted -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [12:00:56] done -141: [12:00:56] ------------------------------------- -141: [12:00:56] Testing calcEnergy with passed coords. -69: Test -69: -69: RP-6306_3d.mrv -69: -69: Test -69: -69: Sotorasib_atrop1.mrv -69: -69: Test -69: -69: Sotorasib_atrop2.mrv -69: -69: Test -69: -69: Sotorasib_atrop3.mrv -69: -69: Test -69: -69: Sotorasib_atrop4.mrv -69: -69: Test -69: -69: Sotorasib_atrop5.mrv -69: -69: [12:00:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [12:00:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +142: [09:20:41] ------------------------------------- +142: [09:20:41] Test MMFF multithreading +89: [09:20:41] Explicit valence for atom # 27 P, 6, is greater than permitted +143: [09:20:41] ------------------------------------- +143: [09:20:41] Test UFF atom labels. +143: [09:20:41] done +143: [09:20:41] ------------------------------------- +143: [09:20:41] Test UFF atom typer. +143: [09:20:41] done +143: [09:20:41] ------------------------------------- +143: [09:20:41] Testing UFF builder tools. +143: [09:20:41] done +143: [09:20:41] ------------------------------------- +143: [09:20:41] Testing UFF builder+minimization. 142: processing 142: launch :0 142: launch :1 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 142: launch :2 142: launch :3 142: launch :4 @@ -25085,11 +26486,9 @@ 142: launch :11 142: launch :12 142: launch :13 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 142: launch :14 142: launch :15 142: launch :16 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 142: launch :17 142: launch :18 142: launch :19 @@ -25097,743 +26496,754 @@ 142: launch :21 142: launch :22 142: launch :23 -69: Test -69: -69: Sotorasib_atropBad1.mrv -69: -69: [12:00:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -141: [12:00:56] done -141: [12:00:56] ------------------------------------- -141: [12:00:56] Testing calcGrad. -69: Test -69: -69: Sotorasib_atropBad2.mrv -69: -69: [12:00:56] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 300 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] 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: [12:00:56] test on : 365 molecules done -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -121: =>start test WHIM -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -121: [12:00:56] test on : 365 molecules done -104/235 Test #121: testWHIM ............................... Passed 0.91 sec +89: =============================================================================== +89: All tests passed (21562 assertions in 3 test cases) +89: +124/235 Test #89: multithreadedSupplierCatchTest ......... Passed 14.54 sec +test 144 + Start 144: testCrystalForceField + +144: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField +144: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF +144: Test timeout computed to be: 1500 +144: ------------------------------------- +144: Test CrystalFF torsional term. +125/235 Test #134: pyTestMHFP ............................. Passed 2.96 sec +test 145 + Start 145: pyForceFieldHelpers + +145: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" +145: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap +145: Test timeout computed to be: 1500 +130: [09:20:41] done +130: [09:20:41] ------------------------------------- +130: [09:20:41] Test GitHub Issue #6958 +130: [09:20:41] DEPRECATION WARNING: please use AtomPairGenerator +126/235 Test #130: testFingerprintGenerators .............. Passed 3.69 sec test 146 Start 146: testDistGeomHelpers 146: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 146: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers 146: Test timeout computed to be: 1500 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [12:00:56] done -141: [12:00:56] ------------------------------------- -141: [12:00:56] Testing Issue242. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [12:00:56] done -141: [12:00:56] ------------------------------------- -141: [12:00:56] Testing github 308: crash during MMFF parameterization . -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [12:00:56] ------------------------------------- -141: [12:00:56] Testing SFIssue1653802. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [12:00:56] done -143: [12:00:56] ------------------------------------- -143: [12:00:56] Testing UFF special cases. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [12:00:56] done -141: [12:00:56] ------------------------------------- -141: [12:00:56] Testing SFIssue2378119. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [12:00:56] UFFTYPER: Unrecognized charge state for atom: 0 -68: ..... -143: [12:00:56] done -143: [12:00:56] ------------------------------------- -143: [12:00:56] Testing Issue239. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: ---------------------------------------------------------------------- -68: Ran 19 tests in 1.149s -68: -68: OK -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: Test -69: -69: Sotorasib_3d.mrv -69: -69: Test -69: -69: ZM374979_atrop1.mrv -69: -69: Test -69: -69: ZM374979_atrop2.mrv -69: -69: Test -69: -69: ZM374979_atrop3.mrv -69: -69: Test -69: -69: ZM374979_atropBad1.mrv -69: -69: [12:00:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -141: [12:00:56] done -141: [12:00:56] ------------------------------------- -141: [12:00:56] Test MMFF force-field parameter getters. -141: [12:00:56] ------------------------------------- -141: [12:00:56] Test MMFF multithreading -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [12:00:56] done -143: [12:00:56] ------------------------------------- -143: [12:00:56] Testing calcEnergy with passed coords. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [12:00:56] done -120: [12:00:56] ------------------------------------- -120: [12:00:56] PMI edge cases. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [12:00:56] done -120: [12:00:56] ------------------------------------- -120: [12:00:56] NPR edge cases. -120: [12:00:56] done -120: [12:00:56] ------------------------------------- -120: [12:00:56] 3D descriptors. -120: [12:00:56] done -120: [12:00:56] ------------------------------------- -120: [12:00:56] 3D descriptor edge cases. -120: [12:00:56] done -120: [12:00:56] ------------------------------------- -120: [12:00:56] Inertial shape factor. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: generating reference data -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [12:00:56] done -105/235 Test #120: test3D ................................. Passed 1.05 sec -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +146: [09:20:41] ******************************************************** +146: [09:20:41] Testing DistGeomHelpers +146: [09:20:41] --------------------------------- +146: [09:20:41] test2 +146: +146: go +146: ------------------------------------- +146: +143: [09:20:42] done +143: [09:20:42] ------------------------------------- +143: [09:20:42] Testing UFF special cases. +143: [09:20:42] UFFTYPER: Unrecognized charge state for atom: 0 +143: [09:20:42] done +143: [09:20:42] ------------------------------------- +143: [09:20:42] Testing Issue239. +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 17.282s +12: +12: OK +143: [09:20:42] done +143: [09:20:42] ------------------------------------- +143: [09:20:42] Testing calcEnergy with passed coords. +126: Warning: Atom Count for residue ARG64A does not match expected count +143: [09:20:42] done +143: [09:20:42] ------------------------------------- +143: [09:20:42] Testing calcGrad. +142: done +143: [09:20:42] done +143: [09:20:42] ------------------------------------- +143: [09:20:42] Testing SFIssue1653802. +143: [09:20:42] done +143: [09:20:42] ------------------------------------- +143: [09:20:42] Testing SFIssue2378119. +142: [09:20:42] done +143: [09:20:42] done +143: [09:20:42] ------------------------------------- +143: [09:20:42] Test UFF force-field parameter getters. +143: [09:20:42] ------------------------------------- +143: [09:20:42] Testing handling missing parameters. +143: [09:20:42] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [09:20:42] UFFTYPER: Unrecognized atom type: Cu+1 (0) +127/235 Test #12: pyBV ................................... Passed 18.35 sec test 147 Start 147: distGeomHelpersCatch 147: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 147: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers 147: Test timeout computed to be: 1500 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [12:00:56] done -143: [12:00:56] ------------------------------------- -143: [12:00:56] Testing calcGrad. -146: [12:00:56] ******************************************************** -146: [12:00:56] Testing DistGeomHelpers -146: [12:00:56] --------------------------------- -146: [12:00:56] test2 -146: -146: go -146: ------------------------------------- -146: -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: Test -69: -69: mrtx1719_3d.mrv -69: -69: Test -69: -69: mrtx1719_atrop1.mrv -69: -69: Test -69: -69: mrtx1719_atrop2.mrv -69: -69: Test -69: -69: mrtx1719_atrop3.mrv -69: -69: Test -69: -69: mrtx1719_atropBad1.mrv -69: -69: [12:00:56] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [12:00:56] done -143: [12:00:56] ------------------------------------- -143: [12:00:56] Testing SFIssue1653802. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [12:00:56] done -143: [12:00:56] ------------------------------------- -143: [12:00:56] Testing SFIssue2378119. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [12:00:56] done -143: [12:00:56] ------------------------------------- -143: [12:00:56] Test UFF force-field parameter getters. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [12:00:56] ------------------------------------- -143: [12:00:56] Testing handling missing parameters. -143: [12:00:56] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [12:00:56] UFFTYPER: Unrecognized atom type: Cu+1 (0) -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [12:00:56] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [12:00:56] UFFTYPER: Unrecognized atom type: Cu+1 (0) -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 400 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [12:00:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [12:00:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [12:00:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [12:00:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [12:00:56] done -143: [12:00:56] ------------------------------------- -143: [12:00:56] Testing SFIssue3009337. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -106/235 Test #144: testCrystalForceField .................. Passed 0.41 sec +143: [09:20:42] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [09:20:42] UFFTYPER: Unrecognized atom type: Cu+1 (0) +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test Issue252: Bad definitions for Crippen atom types. +147: Randomness seeded to: 2221402102 +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test calculation of ChiVs. +143: [09:20:42] done +143: [09:20:42] ------------------------------------- +143: [09:20:42] Testing SFIssue3009337. +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test calculation of ChiNs. +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test calculation of HallKierAlpha. +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test calculation of Kappa1. +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test calculation of Kappa2. +143: [09:20:42] done +143: [09:20:42] ------------------------------------- +143: [09:20:42] Test UFF multithreading +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test calculation of Kappa3. +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test Crippen atom type calculations. +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test ring descriptors +128/235 Test #144: testCrystalForceField .................. Passed 0.93 sec +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test other count descriptors. test 148 Start 148: pyDistGeomHelpers 148: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 148: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 148: Test timeout computed to be: 1500 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: Randomness seeded to: 4276516629 -143: [12:00:56] done -143: [12:00:56] ------------------------------------- -143: [12:00:56] Test UFF multithreading -70: [12:00:56] deprecated group abbreviation ignored on line 24 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -70: [12:00:56] -70: -70: **** -70: Post-condition Violation -70: Element 'Mv' not found -70: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -70: Failed Expression: anum > -1 -70: ---------- -70: Stacktrace: -70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 3# 0x00007F77AB6C8391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 4# 0x00007F77AB6D1CFA in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 5# 0x00007F77AB6D207D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 9# 0x0000558932464CF5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 10# 0x00005589324CB4F2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 11# 0x000055893244B963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 12# 0x00007F77AAC33D68 in /lib/x86_64-linux-gnu/libc.so.6 -70: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -70: 14# 0x000055893244BB11 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: ---------- -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: **** -70: -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: generating reference data -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -123: =>start test autocorr3D -123: [12:00:56] test on : 365 molecules done -134: .. -134: ---------------------------------------------------------------------- -134: Ran 2 tests in 0.114s -134: -134: OK -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -107/235 Test #123: testAUTOCORR3D ......................... Passed 1.01 sec +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test MQN +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test GitHub Issue 56. +111: [09:20:42] WARNING: not removing hydrogen atom without neighbors +111: [09:20:42] WARNING: not removing hydrogen atom without neighbors +111: [09:20:42] WARNING: not removing hydrogen atom without neighbors +111: [09:20:42] WARNING: not removing hydrogen atom without neighbors +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test Github92: Bad Crippen atom type for pyrrole H. +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test Github362: order dependence in Kier-Hall descriptors. +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test calculation of spiro and bridgehead counts. +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test Github694: ExactMolWt ignoring the mass of the electron +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Testing Properties and KitchenSink +111: [09:20:42] ---Caught keyerror (bad property name)--- +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test USR Descriptor +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test Github #1973: support P and S terms for TPSA calculation +111: [09:20:42] done +111: [09:20:42] ------------------------------------- +111: [09:20:42] Test Github #2948: Empty molecule has non-zero LabuteASA +111: [09:20:42] done +129/235 Test #111: testDescriptors ........................ Passed 12.02 sec +147: [09:20:42] [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: [09:20:42] [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)] test 149 Start 149: testMolAlign 149: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 149: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 149: Test timeout computed to be: 1500 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108/235 Test #68: pyDepictor ............................. Passed 1.93 sec +147: [09:20:42] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [09:20:42] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] +147: [09:20:42] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] +145: [09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: generating reference data +147: [09:20:42] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +145: [09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: ..[09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +147: [09:20:42] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +147: [09:20:42] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [09:20:42] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [09:20:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +147: ----------- +130/235 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 1.46 sec test 150 Start 150: testO3AAlign 150: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 150: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 150: Test timeout computed to be: 1500 -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: pass 2 -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -89: [12:00:56] Explicit valence for atom # 2 O, 4, is greater than permitted -133: .............. -133: ---------------------------------------------------------------------- -133: Ran 14 tests in 0.239s -133: -133: OK -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [12:00:56] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [12:00:56] Explicit valence for atom # 3 Be, 4, is greater than permitted -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:56] 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: [12:00:57] test on : 365 molecules done -109/235 Test #118: testRDF ................................ Passed 1.38 sec +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [09:20:42] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [09:20:42] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] +147: ----------- +145: .[09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [09:20:42] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +147: ----------- +147: ----------- +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [09:20:42] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [09:20:42] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [09:20:42] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [09:20:42] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [09:20:42] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [09:20:42] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +145: .[09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +147: [09:20:42] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +145: .[09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +147: [09:20:42] UFFTYPER: Unrecognized charge state for atom: 1 +147: [09:20:42] UFFTYPER: Unrecognized charge state for atom: 1 +145: .[09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[09:20:42] UFFTYPER: Unrecognized hybridization for atom: 0 +145: [09:20:42] UFFTYPER: Unrecognized atom type: Cu+1 (0) +145: .[09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[09:20:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +147: [09:20:42] UFFTYPER: Unrecognized charge state for atom: 1 +145: ...[09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +145: [09:20:42] Molecule does not have explicit Hs. Consider calling AddHs() +149: *********************************************************** +149: Testing MolAlign +149: --------------------------------- +149: test1MolAlign +149: +149: --------------------------------- +149: test1GetBestRMS +149: +149: --------------------------------- +149: test1MolWithQueryAlign +149: +149: --------------------------------- +149: test2AtomMap +149: +149: --------------------------------- +149: test3Weights +149: +149: --------------------------------- +149: testIssue241 +149: +149: *********************************************************** +131/235 Test #149: testMolAlign ........................... Passed 0.46 sec test 151 Start 151: molAlignCatchTest 151: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 151: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 151: Test timeout computed to be: 1500 -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -142: done -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [12:00:57] Explicit valence for atom # 27 P, 6, is greater than permitted -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [12:00:57] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [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)] -69: Test -69: -69: FalseAtropisomer.mrv -69: -69: Test -69: -69: AtropEnhancedStereo.mrv -69: -69: Test -69: -69: AtropManyChirals.mrv -69: -69: Test -69: -69: AtropManyChiralsEnhanced.mrv -69: -69: Test -69: -69: AtropManyChiralsEnhanced2.mrv -69: -69: Test -69: -69: AtropManyChiralsEnhanced3.mrv -69: -69: Test -69: -69: AtropManyChiralsEnhanced4.mrv -69: -69: Test -69: -69: BMS-986142_3d_chiral.mrv -69: -69: Test -69: -69: BMS-986142_3d.mrv -69: -69: Test -69: -69: BMS-986142_atrop1.mrv -69: -69: Test -69: -69: BMS-986142_atrop2.mrv -69: -69: Test -69: -69: BMS-986142_atrop3.mrv -69: -69: Test -69: -69: BMS-986142_atrop4.mrv -69: -69: Test -69: -69: BMS-986142_atrop5.mrv -69: -69: [12:00:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [12:00:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [12:00:57] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:00:57] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [12:00:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] -147: [12:00:57] [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)] -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [12:00:57] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [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)] -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [12:00:57] [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)] -142: [12:00:57] done -147: [12:00:57] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [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)] -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: Elapsed time: 1.46123 s -115: Errors:0 -115: [12:00:57] test on : 500 molecules done -147: [12:00:57] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [12:00:57] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:00:57] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:00:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [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)] -130: [12:00:57] done -130: [12:00:57] ------------------------------------- -130: [12:00:57] Test unfolded version of RDKFP -130: [12:00:57] ------------------------------------- -130: [12:00:57] Test topological torsion fp generator -130: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -110/235 Test #115: testEEM ................................ Passed 1.52 sec -130: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator +145: ... +145: ---------------------------------------------------------------------- +145: Ran 19 tests in 0.497s +145: +145: OK +147: [09:20:43] UFFTYPER: Unrecognized charge state for atom: 5 +147: [09:20:43] UFFTYPER: Unrecognized charge state for atom: 5 +147: [09:20:43] UFFTYPER: Unrecognized charge state for atom: 5 +132/235 Test #145: pyForceFieldHelpers .................... Passed 1.46 sec test 152 Start 152: pyMolAlign 152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 152: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap 152: Test timeout computed to be: 1500 -130: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -69: Test -69: -69: BMS-986142_atrop6.mrv -69: -69: Test -69: -69: BMS-986142_atrop7.mrv -69: -69: Test -69: -69: BMS-986142_atrop8.mrv -69: -69: [12:00:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [12:00:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -147: ----------- -127: ........ -127: ---------------------------------------------------------------------- -127: Ran 8 tests in 0.401s -127: -127: OK -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:00:57] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:00:57] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] -147: [12:00:57] [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: ----------- -125: Warning: Atom Count for residue ASN39A does not match expected count -69: Test -69: -69: BMS-986142_atropBad2.mrv -69: -69: [12:00:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -130: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -147: [12:00:57] [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)] -111/235 Test #134: pyTestMHFP ............................. Passed 0.89 sec +151: Randomness seeded to: 1498213887 +151: 145294936 +151: 150343001 +147: [09:20:43] UFFTYPER: Unrecognized charge state for atom: 6 +147: [09:20:43] UFFTYPER: Unrecognized charge state for atom: 6 +147: [09:20:43] UFFTYPER: Unrecognized charge state for atom: 6 +117: =>start test AUTOCORR3D custom +117: [09:20:43] test on : 365 molecules done +143: processing +143: launch :0 +143: launch :1 +143: launch :2 +143: launch :3 +143: [09:20:44] Rep: 0 Mol:0 +143: [09:20:44] Rep: 0 Mol:3 +143: [09:20:44] Rep: 0 Mol:4 +143: [09:20:44] Rep: 0 Mol:1 +143: [09:20:44] Rep: 0 Mol:5 +143: [09:20:44] Rep: 0 Mol:2 +143: [09:20:44] Rep: 0 Mol:8 +143: [09:20:44] Rep: 0 Mol:12 +143: [09:20:44] Rep: 0 Mol:16 +143: [09:20:44] Rep: 0 Mol:7 +143: [09:20:44] Rep: 0 Mol:11 +143: [09:20:44] Rep: 0 Mol:20 +143: [09:20:44] Rep: 0 Mol:6 +143: [09:20:44] Rep: 0 Mol:24 +143: [09:20:44] Rep: 0 Mol:15 +143: [09:20:44] Rep: 0 Mol:19 +143: [09:20:44] Rep: 0 Mol:28 +143: [09:20:44] Rep: 0 Mol:10 +143: [09:20:44] Rep: 0 Mol:23 +143: [09:20:44] Rep: 0 Mol:27 +143: [09:20:44] Rep: 0 Mol:31 +143: [09:20:44] Rep: 0 Mol:9 +143: [09:20:44] Rep: 0 Mol:13 +148: .[09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +143: [09:20:44] Rep: 0 Mol:17 +143: [09:20:44] Rep: 0 Mol:14 +126: Warning: Atom Count for residue LYS80A does not match expected count +143: [09:20:44] Rep: 0 Mol:18 +143: [09:20:44] Rep: 0 Mol:22 +143: [09:20:44] Rep: 0 Mol:21 +143: [09:20:44] Rep: 0 Mol:26 +143: [09:20:44] Rep: 0 Mol:25 +148: [09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +143: [09:20:44] Rep: 0 Mol:29 +148: [09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +143: [09:20:44] Rep: 0 Mol:30 +148: [09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +141: processing +141: launch :0 +141: launch :1 +141: launch :2 +141: [09:20:44] Rep: 0 Mol:0 +141: [09:20:44] Rep: 0 Mol:1 +141: [09:20:44] Rep: 0 Mol:5 +141: launch :3 +141: [09:20:44] Rep: 0 Mol:9 +141: [09:20:44] Rep: 0 Mol:2 +141: [09:20:44] Rep: 0 Mol:3 +148: [09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:44] Rep: 0 Mol:4 +148: [09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:44] Rep: 0 Mol:13 +141: [09:20:44] Rep: 0 Mol:17 +148: .[09:20:44] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:44] Rep: 0 Mol:6 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:10 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:7 +141: [09:20:45] Rep: 0 Mol:11 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:15 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:19 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:23 +141: [09:20:45] Rep: 0 Mol:27 +141: [09:20:45] Rep: 0 Mol:21 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:8 +141: [09:20:45] Rep: 0 Mol:31 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:25 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:12 +141: [09:20:45] Rep: 0 Mol:29 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:16 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:14 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:18 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:20 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:22 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:26 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:24 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 20 Mol:3 +141: [09:20:45] Rep: 0 Mol:30 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 0 Mol:28 +141: [09:20:45] Rep: 20 Mol:7 +141: [09:20:45] Rep: 20 Mol:11 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:45] Rep: 20 Mol:15 +141: [09:20:45] Rep: 20 Mol:19 +141: [09:20:45] Rep: 20 Mol:23 +141: [09:20:45] Rep: 20 Mol:27 +141: [09:20:45] Rep: 20 Mol:31 +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +75: [09:20:45] Finished: testSmiCorrectness() +75: [09:20:45] ----------------------------------------- +75: +75: [09:20:45] +75: ----------------------------------------- +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +75: [09:20:45] Spurious data before the first property will be ignored +75: [09:20:45] Property will be truncated after the first blank line +75: [09:20:45] Property will be truncated after the first blank line +75: [09:20:45] Property will be truncated after the first blank line +125: Warning: Atom Count for residue GLU150A does not match expected count +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:45] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:46] Rep: 40 Mol:3 +141: [09:20:46] Rep: 40 Mol:7 +141: [09:20:46] Rep: 40 Mol:11 +141: [09:20:46] Rep: 40 Mol:15 +141: [09:20:46] Rep: 40 Mol:19 +141: [09:20:46] Rep: 40 Mol:23 +141: [09:20:46] Rep: 40 Mol:27 +141: [09:20:46] Rep: 40 Mol:31 +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:46] Rep: 20 Mol:1 +141: [09:20:46] Rep: 20 Mol:5 +141: [09:20:46] Rep: 20 Mol:9 +117: =>start test 2 WHIM custom +117: [09:20:46] test on : 365 molecules done +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:46] Rep: 20 Mol:13 +141: [09:20:46] Rep: 20 Mol:17 +141: [09:20:46] Rep: 20 Mol:21 +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:46] Rep: 20 Mol:25 +141: [09:20:46] Rep: 20 Mol:29 +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +125: Warning: Atom Count for residue ASN157A does not match expected count +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:46] Rep: 60 Mol:3 +141: [09:20:46] Rep: 60 Mol:7 +141: [09:20:46] Rep: 60 Mol:11 +141: [09:20:46] Rep: 60 Mol:15 +141: [09:20:46] Rep: 60 Mol:19 +141: [09:20:46] Rep: 60 Mol:23 +141: [09:20:46] Rep: 60 Mol:27 +141: [09:20:46] Rep: 60 Mol:31 +143: [09:20:46] Rep: 100 Mol:0 +143: [09:20:46] Rep: 100 Mol:4 +143: [09:20:46] Rep: 100 Mol:8 +143: [09:20:46] Rep: 100 Mol:12 +143: [09:20:46] Rep: 100 Mol:16 +143: [09:20:46] Rep: 100 Mol:20 +143: [09:20:46] Rep: 100 Mol:24 +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +143: [09:20:46] Rep: 100 Mol:28 +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +143: [09:20:46] Rep: 100 Mol:3 +143: [09:20:46] Rep: 100 Mol:7 +143: [09:20:46] Rep: 100 Mol:11 +143: [09:20:46] Rep: 100 Mol:15 +143: [09:20:46] Rep: 100 Mol:19 +143: [09:20:46] Rep: 100 Mol:23 +143: [09:20:46] Rep: 100 Mol:27 +143: [09:20:46] Rep: 100 Mol:31 +148: [09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[09:20:46] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:47] Rep: 80 Mol:3 +141: [09:20:47] Rep: 80 Mol:7 +141: [09:20:47] Rep: 80 Mol:11 +141: [09:20:47] Rep: 80 Mol:15 +141: [09:20:47] Rep: 80 Mol:19 +141: [09:20:47] Rep: 80 Mol:23 +141: [09:20:47] Rep: 80 Mol:27 +141: [09:20:47] Rep: 80 Mol:31 +141: [09:20:47] Rep: 20 Mol:2 +141: [09:20:47] Rep: 20 Mol:6 +141: [09:20:47] Rep: 20 Mol:10 +141: [09:20:47] Rep: 20 Mol:14 +141: [09:20:47] Rep: 20 Mol:18 +141: [09:20:47] Rep: 20 Mol:22 +141: [09:20:47] Rep: 20 Mol:0 +141: [09:20:47] Rep: 20 Mol:4 +146: [09:20:42] --------------------------------- +146: [09:20:42] test3 +146: +146: [09:20:42] --------------------------------- +146: [09:20:42] test4 +146: +146: [09:20:42] --------------------------------- +146: [09:20:42] test5 +146: +146: [09:20:46] --------------------------------- +146: [09:20:46] test6 +146: +146: [09:20:46] --------------------------------- +146: [09:20:46] test15Dists +146: +146: [09:20:46] --------------------------------- +146: [09:20:46] test Issue 215 +146: +146: [09:20:46] --------------------------------- +146: [09:20:46] testMultipleConfs +146: +146: [09:20:46] --------------------------------- +146: [09:20:46] testMultipleConfsExpTors +146: +146: [09:20:46] --------------------------------- +146: [09:20:46] testIssue227 +146: +146: [09:20:46] --------------------------------- +146: [09:20:46] testIssue236 +146: +146: [09:20:46] --------------------------------- +146: [09:20:46] testOrdering +146: +146: [09:20:46] --------------------------------- +146: [09:20:46] testIssue244 +146: +146: [09:20:46] --------------------------------- +146: [09:20:46] testIssue251 +146: +146: [09:20:46] --------------------------------- +146: [09:20:46] testIssue276 +146: [09:20:46] --------------------------------- +146: [09:20:46] testIssue284 +146: +146: [09:20:46] --------------------------------- +146: [09:20:46] testIssue285 +146: +146: [09:20:46] --------------------------------- +146: [09:20:46] testIssue355 +146: +146: [09:20:46] --------------------------------- +146: [09:20:46] testRandomCoords +146: +146: [09:20:47] --------------------------------- +146: [09:20:47] test sf.net issue 1989539 +146: +146: [09:20:47] --------------------------------- +146: [09:20:47] test sf.net issue 2091864 +146: +146: [09:20:47] --------------------------------- +146: [09:20:47] test constrained embedding +146: +146: [09:20:47] ssd: 0.0752641 +141: [09:20:47] Rep: 20 Mol:26 +141: [09:20:47] Rep: 20 Mol:30 +148: [09:20:47] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:47] Rep: 20 Mol:8 +141: [09:20:47] Rep: 20 Mol:12 +141: [09:20:47] Rep: 20 Mol:16 +146: [09:20:47] ssd: 0.0659363 +141: [09:20:47] Rep: 20 Mol:20 +141: [09:20:47] Rep: 20 Mol:24 +141: [09:20:47] Rep: 20 Mol:28 +75: [09:20:47] Finished: testSDCorrectness() +75: [09:20:47] ----------------------------------------- +75: +133/235 Test #75: testMultithreadedMolSupplier ........... Passed 21.21 sec test 153 Start 153: testFeatures 153: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures 153: Test timeout computed to be: 1500 -147: [12:00:57] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [12:00:57] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] 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: ----------- -130: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -147: ----------- -130: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [12:00:57] done -130: [12:00:57] ------------------------------------- -130: [12:00:57] Test Topological Torsions. -130: [12:00:57] done -130: [12:00:57] ------------------------------------- -130: [12:00:57] Test Folded torsions. -130: [12:00:57] done -130: [12:00:57] ------------------------------------- -130: [12:00:57] Test Bulk Topological Torsions. -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [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)] -112/235 Test #133: pyTestGenerator ........................ Passed 0.99 sec -test 154 - Start 154: pyChemicalFeatures - -154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" -154: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap -154: Test timeout computed to be: 1500 -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [12:00:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:00:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:00:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:00:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:00:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [12:00:57] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -153: [12:00:57] ------------------------------------- -153: [12:00:57] AtomType parser testing. -153: [12:00:57] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -153: [12:00:57] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -153: [12:00:57] done -153: [12:00:57] ------------------------------------- -153: [12:00:57] FeatureDefinition parser testing. -113/235 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.68 sec -153: [12:00:57] done -153: [12:00:57] ------------------------------------- -153: [12:00:57] Test pulling feat defs from a string. -153: [12:00:57] done -153: [12:00:57] ------------------------------------- -153: [12:00:57] FeatureDef functionality testing. -test 155 - Start 155: testShapeHelpers - -155: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers -155: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers -155: Test timeout computed to be: 1500 -151: Randomness seeded to: 4194058297 -151: 81830016 -153: [12:00:57] done -153: [12:00:57] ------------------------------------- -153: [12:00:57] FeatureFactory testing. -153: [12:00:57] 1 -153: [12:00:57] 2 -153: [12:00:57] 3 -153: [12:00:57] 4 -153: [12:00:57] 5 -153: [12:00:57] 6 -153: [12:00:57] done -153: [12:00:57] ------------------------------------- -153: [12:00:57] Feature Location testing. -153: [12:00:57] done -153: [12:00:57] ------------------------------------- -153: [12:00:57] Test building a FeatureFactory from a file -153: [12:00:57] done -153: [12:00:57] ------------------------------------- -153: [12:00:57] Testing Issue 224. -153: [12:00:57] done -153: [12:00:57] ------------------------------------- -153: [12:00:57] Testing Issue 225. -153: [12:00:57] done -153: [12:00:57] ------------------------------------- -153: [12:00:57] Test Issue346 -153: [12:00:57] done -153: [12:00:57] ------------------------------------- -153: [12:00:57] Test Issue347 -153: [12:00:57] done -153: [12:00:57] ------------------------------------- -153: [12:00:57] Testing Issue 348. -153: [12:00:57] SMARTS Parse Error: syntax error while parsing: [C[C] -153: [12:00:57] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -153: [12:00:57] ------------------------------------- -153: [12:00:57] Testing Nested AtomType definitions. +153: [09:20:47] ------------------------------------- +153: [09:20:47] AtomType parser testing. +141: [09:20:47] Rep: 40 Mol:1 +141: [09:20:47] Rep: 40 Mol:5 +141: [09:20:47] Rep: 40 Mol:9 +141: [09:20:47] Rep: 40 Mol:13 +141: [09:20:47] Rep: 40 Mol:17 +153: [09:20:47] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +153: [09:20:47] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' +153: [09:20:47] done +153: [09:20:47] ------------------------------------- +153: [09:20:47] FeatureDefinition parser testing. +153: [09:20:47] done +153: [09:20:47] ------------------------------------- +153: [09:20:47] Test pulling feat defs from a string. +153: [09:20:47] done +153: [09:20:47] ------------------------------------- +153: [09:20:47] FeatureDef functionality testing. +153: [09:20:47] done +153: [09:20:47] ------------------------------------- +153: [09:20:47] FeatureFactory testing. +153: [09:20:47] 1 +153: [09:20:47] 2 +153: [09:20:47] 3 +153: [09:20:47] 4 +153: [09:20:47] 5 +153: [09:20:47] 6 +153: [09:20:47] done +153: [09:20:47] ------------------------------------- +153: [09:20:47] Feature Location testing. +153: [09:20:47] done +153: [09:20:47] ------------------------------------- +153: [09:20:47] Test building a FeatureFactory from a file +153: [09:20:47] done +153: [09:20:47] ------------------------------------- +153: [09:20:47] Testing Issue 224. +153: [09:20:47] done +153: [09:20:47] ------------------------------------- +153: [09:20:47] Testing Issue 225. +153: [09:20:47] done +153: [09:20:47] ------------------------------------- +153: [09:20:47] Test Issue346 +153: [09:20:47] done +153: [09:20:47] ------------------------------------- +153: [09:20:47] Test Issue347 +153: [09:20:47] done +153: [09:20:47] ------------------------------------- +153: [09:20:47] Testing Issue 348. +153: [09:20:47] SMARTS Parse Error: syntax error while parsing: [C[C] +153: [09:20:47] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +153: [09:20:47] ------------------------------------- +153: [09:20:47] Testing Nested AtomType definitions. 153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -153: [12:00:57] ------------------------------------- -153: [12:00:57] Testing Github Issue #252: crash when calling getPos() with no conformer. -153: [12:00:57] expect a precondition failure message below -153: [12:00:57] +153: [09:20:47] ------------------------------------- +153: [09:20:47] Testing Github Issue #252: crash when calling getPos() with no conformer. +153: [09:20:47] expect a precondition failure message below +153: [09:20:47] 153: 153: **** 153: Pre-condition Violation @@ -25846,84 +27256,118 @@ 153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -153: 4# 0x000055912A98AE20 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 5# 0x000055912A97F6A3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 6# 0x00007F8E18A33D68 in /lib/x86_64-linux-gnu/libc.so.6 +153: 4# 0x00005612CFDE2E20 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 5# 0x00005612CFDD76A3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 6# 0x00007F483862ED68 in /lib/x86_64-linux-gnu/libc.so.6 153: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -153: 8# 0x000055912A97F7A1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 8# 0x00005612CFDD77A1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: ---------- 153: **** 153: -153: [12:00:57] Done -153: [12:00:57] ------------------------------------- -153: [12:00:57] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -153: [12:00:57] done -114/235 Test #153: testFeatures ........................... Passed 0.07 sec -test 156 - Start 156: pyShapeHelpers +153: [09:20:47] Done +153: [09:20:47] ------------------------------------- +153: [09:20:47] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +153: [09:20:47] done +141: [09:20:47] Rep: 40 Mol:21 +141: [09:20:47] Rep: 40 Mol:25 +134/235 Test #153: testFeatures ........................... Passed 0.09 sec +test 154 + Start 154: pyChemicalFeatures -156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" -156: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap -156: Test timeout computed to be: 1500 -69: Test -69: -69: JDQ443_3d.mrv -69: -69: Test -69: -69: JDQ443_atrop1.mrv -69: -69: Test -69: -69: JDQ443_atrop2.mrv -69: -69: Test -69: -69: JDQ443_atrop3.mrv -69: -69: Test -69: -69: JDQ443_atropBad1.mrv -69: -69: [12:00:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:00:57] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: .[12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:00:57] DEPRECATION WARNING: please use AtomPairGenerator -70: [12:00:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -70: [12:00:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -126: ..[12:00:57] -126: -126: **** +154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" +154: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap +154: Test timeout computed to be: 1500 +141: [09:20:47] Rep: 40 Mol:29 +117: =>start test 1 WHIM custom +117: [09:20:47] test on : 365 molecules done +143: [09:20:47] Rep: 100 Mol:1 +143: [09:20:47] Rep: 100 Mol:5 +143: [09:20:47] Rep: 100 Mol:9 +143: [09:20:47] Rep: 100 Mol:13 +143: [09:20:47] Rep: 100 Mol:17 +143: [09:20:47] Rep: 100 Mol:21 +143: [09:20:47] Rep: 100 Mol:25 +143: [09:20:47] Rep: 100 Mol:29 +146: [09:20:47] --------------------------------- +146: [09:20:47] test sf.net issue 2091974 +146: +146: [09:20:47] --------------------------------- +146: [09:20:47] test sf.net issue 2835784 +146: +146: [09:20:47] --------------------------------- +146: [09:20:47] test sf.net issue 3019283 +146: +146: [09:20:47] --------------------------------- +146: [09:20:47] test sf.net issue 3238580 +146: +146: [09:20:47] --------------------------------- +146: [09:20:47] test sf.net issue 3483968 +146: +146: [09:20:48] --------------------------------- +146: [09:20:48] test github issue 55 +146: +146: [09:20:48] --------------------------------- +146: [09:20:48] test1 +146: +146: [09:20:48] --------------------------------- +146: [09:20:48] test multi-threading +146: +146: building molecules +141: [09:20:48] Rep: 60 Mol:1 +141: [09:20:48] Rep: 60 Mol:5 +141: [09:20:48] Rep: 60 Mol:9 +141: [09:20:48] Rep: 60 Mol:13 +141: [09:20:48] Rep: 60 Mol:17 +143: [09:20:48] Rep: 100 Mol:2 +143: [09:20:48] Rep: 100 Mol:6 +143: [09:20:48] Rep: 100 Mol:10 +146: generating reference data +143: [09:20:48] Rep: 100 Mol:14 +143: [09:20:48] Rep: 100 Mol:18 +143: [09:20:48] Rep: 100 Mol:22 +143: [09:20:48] Rep: 100 Mol:26 +143: [09:20:48] Rep: 100 Mol:30 +141: [09:20:48] Rep: 60 Mol:21 +141: [09:20:48] Rep: 60 Mol:25 +141: [09:20:48] Rep: 60 Mol:29 +154: .[09:20:48] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[09:20:48] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:48] Rep: 40 Mol:0 +141: [09:20:48] Rep: 40 Mol:4 +141: [09:20:48] Rep: 40 Mol:8 +141: [09:20:48] Rep: 40 Mol:12 +148: [09:20:48] Molecule does not have explicit Hs. Consider calling AddHs() +154: ..[09:20:48] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:48] Rep: 40 Mol:16 +154: .[09:20:48] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[09:20:48] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +154: [09:20:48] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +154: ... +154: ---------------------------------------------------------------------- +154: Ran 9 tests in 0.324s +154: +154: OK +141: [09:20:48] Rep: 40 Mol:20 +141: [09:20:48] Rep: 40 Mol:24 +141: [09:20:48] Rep: 40 Mol:28 +141: [09:20:48] Rep: 40 Mol:2 +141: [09:20:48] Rep: 40 Mol:6 +141: [09:20:48] Rep: 40 Mol:10 +147: [09:20:48] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +141: [09:20:48] Rep: 40 Mol:14 +141: [09:20:48] Rep: 40 Mol:18 +141: [09:20:48] Rep: 40 Mol:22 +141: [09:20:48] Rep: 40 Mol:26 +141: [09:20:48] Rep: 40 Mol:30 +147: [09:20:48] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +135/235 Test #154: pyChemicalFeatures ..................... Passed 1.37 sec +test 155 + Start 155: testShapeHelpers + +155: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers +155: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers +155: Test timeout computed to be: 1500 +147: [09:20:48] UFFTYPER: Warning: hybridization set to SP3 for atom 6 155: *********************************************************** 155: Testing ShapeHelpers 155: --------------------------------- @@ -25936,748 +27380,440 @@ 155: testGithub4364 155: 155: *********************************************************** -69: Test -69: -69: RP-6306_atrop1.mrv -69: -69: Test -69: -69: RP-6306_atrop2.mrv -69: -69: Test -69: -69: RP-6306_atrop3.mrv -69: -69: Test -69: -69: RP-6306_atrop4.mrv -69: -69: Test -69: -69: RP-6306_atrop5.mrv -69: -69: [12:00:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [12:00:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -115/235 Test #155: testShapeHelpers ....................... Passed 0.09 sec +136/235 Test #155: testShapeHelpers ....................... Passed 0.06 sec +test 156 + Start 156: pyShapeHelpers + +156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" +156: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap +156: Test timeout computed to be: 1500 +147: [09:20:49] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: [09:20:49] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: [09:20:49] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +126: Warning: Atom Count for residue GLU150A does not match expected count +122: =>start test GETAWAY +122: [09:20:49] test on : 365 molecules done +141: [09:20:49] Rep: 60 Mol:2 +137/235 Test #122: testGETAWAY ............................ Passed 14.79 sec test 157 Start 157: testMolCatalog 157: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 157: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog 157: Test timeout computed to be: 1500 -151: 80577190 -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-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -126: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -126: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitDescriptors.so.1 -126: 3# 0x00007F7187F059C2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -126: 4# 0x00007F7187F15E16 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -126: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -126: 6# 0x00007F718BED366C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -126: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -126: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -126: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-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-202409.6/obj-x86_64-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-202409.6/obj-x86_64-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-202409.6/obj-x86_64-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-202409.6/obj-x86_64-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-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -126: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -126: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 17# 0x00007F71899B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 18# 0x00007F71899B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 19# 0x00007F71899B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 20# 0x00007F71899B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 21# 0x00007F71899B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -126: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -126: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -126: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -126: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -126: 27# 0x00007F718BED0406 in /lib/x86_64-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# 0x00000000005BEE79 in /usr/bin/python3 -126: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 32# 0x0000000000547080 in /usr/bin/python3 -126: 33# 0x00000000006AB720 in /usr/bin/python3 -126: 34# _PyObject_MakeTpCall in /usr/bin/python3 -126: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 36# 0x00000000005BEE79 in /usr/bin/python3 -126: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 38# 0x0000000000547080 in /usr/bin/python3 -126: 39# 0x00000000006AB720 in /usr/bin/python3 -126: 40# _PyObject_MakeTpCall in /usr/bin/python3 -126: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 42# 0x00000000005BEE79 in /usr/bin/python3 -126: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 44# 0x0000000000547080 in /usr/bin/python3 -126: 45# 0x00000000006AB720 in /usr/bin/python3 -126: 46# _PyObject_MakeTpCall in /usr/bin/python3 -126: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -126: 48# 0x000000000059582E 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# 0x000000000066A861 in /usr/bin/python3 -126: 53# 0x000000000066670C in /usr/bin/python3 -126: 54# 0x000000000067F713 in /usr/bin/python3 -126: 55# 0x000000000067ECE3 in /usr/bin/python3 -126: 56# 0x000000000067EB1E in /usr/bin/python3 -126: 57# Py_RunMain in /usr/bin/python3 -126: 58# Py_BytesMain in /usr/bin/python3 -126: 59# 0x00007F718C79DD68 in /lib/x86_64-linux-gnu/libc.so.6 -126: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -126: 61# _start in /usr/bin/python3 -126: ---------- -126: **** -126: -69: Test -69: -69: RP-6306_atropBad1.mrv -69: -69: [12:00:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -69: Test -69: -69: RP-6306_atropBad2.mrv -69: -69: [12:00:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [12:00:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [12:00:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -149: *********************************************************** -149: Testing MolAlign -149: --------------------------------- -149: test1MolAlign -149: -149: --------------------------------- -149: test1GetBestRMS -149: -149: --------------------------------- -149: test1MolWithQueryAlign -149: -149: --------------------------------- -149: test2AtomMap -149: -149: --------------------------------- -149: test3Weights -149: -149: --------------------------------- -149: testIssue241 -149: -149: *********************************************************** -36: [12:00:57] Maximum BFS search size exceeded. -36: This is likely due to a highly symmetric fused ring system. -116/235 Test #149: testMolAlign ........................... Passed 0.32 sec +141: [09:20:49] Rep: 60 Mol:6 +141: [09:20:49] Rep: 60 Mol:10 +141: [09:20:49] Rep: 60 Mol:14 +141: [09:20:49] Rep: 60 Mol:18 +141: [09:20:49] Rep: 60 Mol:22 +141: [09:20:49] Rep: 60 Mol:26 +141: [09:20:49] Rep: 60 Mol:30 +138/235 Test #157: testMolCatalog ......................... Passed 0.07 sec test 158 Start 158: pyMolCatalog 158: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 158: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 158: Test timeout computed to be: 1500 -117/235 Test #127: pyMolDescriptors3D ..................... Passed 1.25 sec +126: Warning: Atom Count for residue ASN157A does not match expected count +141: [09:20:49] Rep: 80 Mol:1 +141: [09:20:49] Rep: 80 Mol:5 +141: [09:20:49] Rep: 80 Mol:9 +141: [09:20:49] Rep: 80 Mol:13 +141: [09:20:49] Rep: 80 Mol:17 +141: [09:20:49] Rep: 80 Mol:21 +141: [09:20:49] Rep: 80 Mol:25 +141: [09:20:49] Rep: 80 Mol:29 +151: 6342342953 +141: [09:20:50] Rep: 60 Mol:0 +141: [09:20:50] Rep: 60 Mol:4 +141: [09:20:50] Rep: 60 Mol:8 +141: [09:20:50] Rep: 60 Mol:12 +141: [09:20:50] Rep: 60 Mol:16 +141: [09:20:50] Rep: 60 Mol:20 +141: [09:20:50] Rep: 60 Mol:24 +141: [09:20:50] Rep: 60 Mol:28 +141: [09:20:50] Rep: 80 Mol:2 +141: [09:20:50] Rep: 80 Mol:6 +141: [09:20:50] Rep: 80 Mol:10 +141: [09:20:50] Rep: 80 Mol:14 +141: [09:20:50] Rep: 80 Mol:18 +141: [09:20:50] Rep: 80 Mol:22 +141: [09:20:50] Rep: 80 Mol:26 +141: [09:20:50] Rep: 80 Mol:30 +148: [09:20:50] Molecule does not have explicit Hs. Consider calling AddHs() +158: . +158: ---------------------------------------------------------------------- +158: Ran 1 test in 0.050s +158: +158: OK +139/235 Test #158: pyMolCatalog ........................... Passed 1.54 sec test 159 Start 159: moldraw2DTest1 159: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 159: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 159: Test timeout computed to be: 1500 -139: ........ -139: ---------------------------------------------------------------------- -139: Ran 8 tests in 0.131s -139: -139: OK -126: ...Warning: Atom Count for residue GLU5A does not match expected count -118/235 Test #157: testMolCatalog ......................... Passed 0.07 sec +159: ----------------- Test 1 +159: file test1_5.svg gave hash 2383324771U not the expected 2811480876U +159: Done +159: ----------------- Test 2 +159: file test2_1.png gave hash 3164573255U not the expected 638584804U +141: [09:20:51] Rep: 80 Mol:0 +141: [09:20:51] Rep: 80 Mol:4 +141: [09:20:51] Rep: 80 Mol:8 +159: file test2_2.png gave hash 3715219030U not the expected 610424244U +141: [09:20:51] Rep: 80 Mol:12 +141: [09:20:51] Rep: 80 Mol:16 +141: [09:20:51] Rep: 80 Mol:20 +141: [09:20:51] Rep: 80 Mol:24 +159: Done +159: ----------------- Test 4 +159: file test4_1.png gave hash 3656546255U not the expected 3993974247U +159: Done +159: ----------------- Test 5 +141: [09:20:51] Rep: 80 Mol:28 +159: file test5_1.png gave hash 3659160374U not the expected 571291290U +159: file test5_2.png gave hash 3029052427U not the expected 97265124U +159: file test5_3.png gave hash 979411683U not the expected 606188176U +159: Done +159: ----------------- Test 6 (atom labels) +159: Done +159: ----------------- Test 7 (backgrounds) +159: file test7_1.png gave hash 37955190U not the expected 1322246680U +156: . +156: ---------------------------------------------------------------------- +156: Ran 1 test in 0.692s +156: +156: OK +156: Testing Shape Helpers wrapper +159: file test7_2.png gave hash 280222352U not the expected 1499012715U +159: Done +159: ----------------- Test8: PrepareMolDrawing +159: Done +159: ----------------- Test multi-threaded drawing +159: reading molecules +159: generating reference drawings +159: processing +159: launch :0 +159: launch :1 +159: launch :2 +159: launch :3 +143: [09:20:51] done +143: [09:20:51] ------------------------------------- +143: [09:20:51] Test UFF multithreading2 +140/235 Test #156: pyShapeHelpers ......................... Passed 3.12 sec test 160 Start 160: moldraw2DTestCatch 160: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 160: Test timeout computed to be: 1500 -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 -145: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -126: Warning: Atom Count for residue GLU150A does not match expected count -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: ..[12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -126: Warning: Atom Count for residue ASN157A does not match expected count -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -69: Test -69: -69: RP-6306_3d.mrv -69: -69: Test -69: -69: Sotorasib_atrop1.mrv -69: -69: Test -69: -69: Sotorasib_atrop2.mrv -69: -69: Test -69: -69: Sotorasib_atrop3.mrv -69: -69: Test -69: -69: Sotorasib_atrop4.mrv -69: -69: Test -69: -69: Sotorasib_atrop5.mrv -69: -69: [12:00:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [12:00:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: Test -69: -69: Sotorasib_atropBad1.mrv -69: -69: [12:00:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -145: .[12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -159: ----------------- Test 1 -69: Test -69: -69: Sotorasib_atropBad2.mrv -69: -69: [12:00:57] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -147: [12:00:57] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -160: Randomness seeded to: 412881245 +160: Randomness seeded to: 2709033607 160: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U -36: F/C=C/Cl -36: [H]/C(F)=C(/[H])Cl -36: F/C=C/Cl -36: F/C=C/Cl -36: C/C(F)=C(/C)Cl -147: [12:00:57] UFFTYPER: Unrecognized charge state for atom: 1 -70: ---------------------------------- -70: ---------------------------------- -70: [12:00:57] -70: -70: **** -70: Pre-condition Violation -70: rlabel out of range for MDL files -70: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp -70: Failed Expression: rlabel >= 0 && rlabel < 100 -70: ---------- -70: Stacktrace: -70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -70: 3# 0x00005589324720FF in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 4# 0x00005589324CB56A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 5# 0x000055893244B963 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 6# 0x00007F77AAC33D68 in /lib/x86_64-linux-gnu/libc.so.6 -70: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -70: 8# 0x000055893244BB11 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: ---------- -70: **** -70: -147: [12:00:57] UFFTYPER: Unrecognized charge state for atom: 1 -70: [12:00:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -119/235 Test #139: pyMolTransforms ........................ Passed 1.03 sec +160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U +160: file contourMol_2.svg gave hash 4241964660U 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 3954963517U not the expected 3792684719U +141: [09:20:52] done +141: [09:20:52] ------------------------------------- +141: [09:20:52] Test MMFF multithreading2 +160: file testGithub3226_1.png gave hash 3357385997U not the expected 3165135374U +160: file testGithub3226_2.png gave hash 1415443727U not the expected 643975155U +160: file testGithub3226_3.png gave hash 2009594401U not the expected 3119571946U +160: file testPNGMetadata_1.png gave hash 1215431680U not the expected 997629701U +151: 2563466584 +151: =============================================================================== +151: All tests passed (73 assertions in 3 test cases) +151: +141/235 Test #151: molAlignCatchTest ...................... Passed 9.80 sec test 161 Start 161: moldraw2DRxnTest1 161: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 161: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 161: Test timeout computed to be: 1500 -160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U -159: file test1_5.svg gave hash 2383324771U not the expected 2811480876U -147: [12:00:57] UFFTYPER: Unrecognized charge state for atom: 1 -141: processing -141: launch :0 -141: [12:00:57] Rep: 0 Mol:0 -160: file contourMol_2.svg gave hash 4241964660U not the expected 1815941817U -141: launch :1 -141: launch :2 -141: launch :3 -36: [12:00:57] ----------------------- -36: Testing isRingFused -159: Done -159: ----------------- Test 2 -141: [12:00:57] Rep: 0 Mol:1 -125: Warning: Atom Count for residue GLU53A does not match expected count -141: [12:00:57] Rep: 0 Mol:5 -141: [12:00:57] Rep: 0 Mol:2 -141: [12:00:57] Rep: 0 Mol:3 -69: Test -69: -69: Sotorasib_3d.mrv -69: -69: Test -69: -69: ZM374979_atrop1.mrv -69: -69: Test -69: -69: ZM374979_atrop2.mrv -69: -69: Test -69: -69: ZM374979_atrop3.mrv -69: -69: Test -69: -69: ZM374979_atropBad1.mrv -69: -69: [12:00:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U -120/235 Test #36: graphmolMolOpsTest ..................... Passed 2.68 sec -145: .[12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:00:57] Rep: 0 Mol:4 +161: ----------------- Test 1 +160: file testPNGMetadata_2.png gave hash 421119850U not the expected 1797853056U +161: file rxn_test1_1.png gave hash 196847225U not the expected 801892091U +161: file rxn_test1_2.png gave hash 1760761969U not the expected 507435337U +161: file rxn_test1_3.png gave hash 3097655468U not the expected 1590809137U +161: file rxn_test1_4.png gave hash 1178565194U not the expected 1766700542U +148: [09:20:53] Molecule does not have explicit Hs. Consider calling AddHs() +161: file rxn_test1_5.png gave hash 2486693442U not the expected 2552100594U +161: file rxn_test1_6.png gave hash 3683203876U not the expected 3791582903U +161: file rxn_test1_7.png gave hash 1361790131U not the expected 1461397406U +161: file rxn_test1_7.svg gave hash 2324077060U not the expected 1831465890U +161: Done +161: ----------------- Test 2: some examples that caused problems in testing +161: file rxn_test2_1.png gave hash 700636031U not the expected 3551633840U +161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C +161: file rxn_test2_2_1.png gave hash 766587530U 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 +143: [09:20:53] done +143: [09:20:53] ------------------------------------- +143: [09:20:53] Test UFF multithreading3 +161: file rxn_test2_2_2.png gave hash 1252117625U 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 +161: file rxn_test2_2_3.png gave hash 3797481496U 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 1813989566U not the expected 1230108677U +160: [09:20:53] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:20:53] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +161: Done +161: ----------------- Test 3: test reactant highlighting +160: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U +160: [09:20:53] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:20:53] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +161: file rxn_test3_1.png gave hash 887759826U not the expected 4189980366U +160: file testHandDrawn-1.png gave hash 2810773836U not the expected 3894611804U +161: Done +161: ----------------- Test 4: some examples from SMARTS in testing +161: draw! +160: [09:20:53] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:20:53] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-2.svg gave hash 1534109833U not the expected 794717511U +160: [09:20:53] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:20:53] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +161: file rxn_test4_1.png gave hash 2871076982U not the expected 2745201873U +160: file testHandDrawn-2.png gave hash 3255836690U not the expected 1443443188U +160: [09:20:53] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:20:53] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U +160: [09:20:53] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:20:53] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-3.png gave hash 1999104941U not the expected 865629432U +160: [09:20:53] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:20:53] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +161: done +160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U +160: [09:20:54] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:20:54] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-4.png gave hash 1317783250U not the expected 3919767093U +117: =>start test GETAWAY custom +117: [09:20:54] test on : 365 molecules done +142/235 Test #117: testRDFcustom .......................... Passed 21.77 sec test 162 Start 162: pyMolDraw2D 162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" 162: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap 162: Test timeout computed to be: 1500 -141: [12:00:57] Rep: 0 Mol:9 -160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U -160: file contourMol_5.svg gave hash 3954963517U not the expected 3792684719U -159: file test2_1.png gave hash 3164573255U not the expected 638584804U -109: [12:00:57] -109: -109: **** -109: Invariant Violation -109: nonsense -109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -109: Failed Expression: token != tokens.end() -109: ---------- -109: Stacktrace: -109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x00007FF4AFE0CDFD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000561B79BED183 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000561B79BEA731 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007FF4AF033D68 in /lib/x86_64-linux-gnu/libc.so.6 -109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -109: 8# 0x0000561B79BEA861 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: ---------- -109: **** -109: -109: [12:00:57] -109: -109: **** -109: Invariant Violation -109: nonsense no new line -109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -109: Failed Expression: token != tokens.end() -109: ---------- -109: Stacktrace: -109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x00007FF4AFE0CDFD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000561B79BED183 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000561B79BEA731 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007FF4AF033D68 in /lib/x86_64-linux-gnu/libc.so.6 -109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -109: 8# 0x0000561B79BEA861 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: ---------- -109: **** -109: -109: [12:00:57] -109: -109: **** -109: Invariant Violation -109: nonsense with tab -109: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -109: Failed Expression: token != tokens.end() -109: ---------- -109: Stacktrace: -109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x00007FF4AFE0CDFD in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000561B79BED183 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000561B79BEA731 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007FF4AF033D68 in /lib/x86_64-linux-gnu/libc.so.6 -109: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -109: 8# 0x0000561B79BEA861 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: ---------- -109: **** -109: -130: [12:00:57] done -130: [12:00:57] ------------------------------------- -130: [12:00:57] Test Rooted Topological Torsions. -130: [12:00:57] done -130: [12:00:57] ------------------------------------- -130: [12:00:57] Test ignoring atoms in Topological Torsions. -130: [12:00:57] done -130: [12:00:57] ------------------------------------- -130: [12:00:57] ------------------------------------- -130: [12:00:57] Test Topological Torsions including info about chirality. -130: [12:00:57] done -130: [12:00:57] ------------------------------------- -130: [12:00:57] Test GitHub Issue 25: fingerprint backwards compatibility. -121/235 Test #109: testFragCatalog ........................ Passed 2.06 sec -130: [12:00:57] done -130: [12:00:57] ------------------------------------- -130: [12:00:57] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -130: [12:00:57] done -130: [12:00:57] ------------------------------------- -130: [12:00:57] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +161: file rxn_test4_2.png gave hash 424710428U not the expected 3094925886U +161: Done +143/235 Test #161: moldraw2DRxnTest1 ...................... Passed 1.66 sec test 163 Start 163: testFMCS 163: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/testFMCS 163: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS 163: Test timeout computed to be: 1500 -130: [12:00:57] done -130: [12:00:57] ------------------------------------- -130: [12:00:57] Test convenience and bulk fp calculation functions -141: [12:00:57] Rep: 0 Mol:13 -159: file test2_2.png gave hash 3715219030U not the expected 610424244U -143: processing -143: launch :0 -143: [12:00:57] Rep: 0 Mol:0 -141: [12:00:57] Rep: 0 Mol:8 -145: .[12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -136: ....... -136: ---------------------------------------------------------------------- -136: Ran 7 tests in 0.349s -136: -136: OK -143: launch :1 -143: launch :2 -143: launch :3 -141: [12:00:57] Rep: 0 Mol:17 -143: [12:00:57] Rep: 0 Mol:1 -143: [12:00:57] Rep: 0 Mol:2 -143: [12:00:57] Rep: 0 Mol:3 -143: [12:00:57] Rep: 0 Mol:4 -143: [12:00:57] Rep: 0 Mol:5 -141: [12:00:57] Rep: 0 Mol:12 -161: ----------------- Test 1 -126: Warning: Atom Count for residue GLU5A does not match expected count -141: [12:00:57] Rep: 0 Mol:6 -143: [12:00:57] Rep: 0 Mol:9 -141: [12:00:57] Rep: 0 Mol:16 -160: file testGithub3226_1.png gave hash 3357385997U not the expected 3165135374U -141: [12:00:57] Rep: 0 Mol:10 -160: file testGithub3226_2.png gave hash 1415443727U not the expected 643975155U -143: [12:00:57] Rep: 0 Mol:6 -143: [12:00:57] Rep: 0 Mol:10 -159: Done -159: ----------------- Test 4 -143: [12:00:57] Rep: 0 Mol:13 -143: [12:00:57] Rep: 0 Mol:7 -143: [12:00:57] Rep: 0 Mol:11 -69: Test -69: -69: mrtx1719_3d.mrv -69: -69: Test -69: -69: mrtx1719_atrop1.mrv -69: -69: Test -69: -69: mrtx1719_atrop2.mrv -69: -69: Test -69: -69: mrtx1719_atrop3.mrv -69: -69: Test -69: -69: mrtx1719_atropBad1.mrv -69: -69: [12:00:57] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -143: [12:00:57] Rep: 0 Mol:8 -141: [12:00:57] Rep: 0 Mol:20 -160: file testGithub3226_3.png gave hash 2009594401U not the expected 3119571946U -143: [12:00:57] Rep: 0 Mol:15 -143: [12:00:57] Rep: 0 Mol:19 -122/235 Test #136: pyPartialCharges ....................... Passed 1.21 sec +148: [09:20:54] Molecule does not have explicit Hs. Consider calling AddHs() +141: [09:20:54] done +141: [09:20:54] ------------------------------------- +141: [09:20:54] Test MMFF multithreading3 +143: [09:20:54] done +143: [09:20:54] ------------------------------------- +143: [09:20:54] Testing GitHubIssue62. +143: [09:20:54] beta-lactam 39.6387 +143: [09:20:54] cyclopropanone 174.698 +143: [09:20:54] aziridine 337.986 +143: [09:20:54] aziridinone 115.248 +143: [09:20:54] isobutene 2.48217 +143: [09:20:54] acetone 1.91788 +143: [09:20:54] cyclopentanone 10.1648 +143: [09:20:54] cyclopropene 99.4921 +143: [09:20:54] cyclobutene 41.0156 +143: [09:20:55] cyclopropane 267.236 +143: [09:20:55] gamma-lactam 15.7471 +143: [09:20:55] trans-2,3-diphenylcyclopropan-1-one 203.398 +128: [09:20:55] done +128: [09:20:55] ------------------------------------- +128: [09:20:55] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +162: ...[09:20:55] Font file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +162: [09:20:55] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +128: [09:20:55] done +128: [09:20:55] ------------------------------------- +128: [09:20:55] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +128: [09:20:55] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:55] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] done +128: [09:20:55] ------------------------------------- +128: [09:20:55] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +128: [09:20:55] done +128: [09:20:55] ------------------------------------- +128: [09:20:55] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] done +128: [09:20:55] ------------------------------------- +128: [09:20:55] Test unfolded version of RDKFP +128: [09:20:55] ------------------------------------- +128: [09:20:55] 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: [09:20:55] ------------------------------------- +128: [09:20:55] Single atoms setting radius 1 bits in Morgan fingerprints +128: [09:20:55] done +128: [09:20:55] ------------------------------------- +128: [09:20:55] Github #879: Pattern fingerprint should set bits for single-atom fragments. +128: [09:20:55] done +128: [09:20:55] ------------------------------------- +128: [09:20:55] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +128: [09:20:55] done +128: [09:20:55] ------------------------------------- +128: [09:20:55] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +128: [09:20:55] done +128: [09:20:55] ------------------------------------- +128: [09:20:55] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +128: [09:20:55] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:55] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:55] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:55] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:55] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:55] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:55] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:55] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:55] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:55] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:55] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:55] DEPRECATION WARNING: please use AtomPairGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [09:20:55] done +128: [09:20:55] ------------------------------------- +128: [09:20:55] Github #2115: BitInfo not complete for RDKFingerprint +128: [09:20:55] done +128: [09:20:55] ------------------------------------- +128: [09:20:55] Github #3723: Fingerprint crash for mols with Zero order bonds +128: [09:20:55] done +143: [09:20:55] cis-2,3-diphenylcyclopropan-1-one 206.852 +144/235 Test #128: testFingerprints ....................... Passed 18.11 sec test 164 Start 164: pyFMCS 164: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Wrap/testFMCS.py" 164: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap 164: Test timeout computed to be: 1500 -143: [12:00:57] Rep: 0 Mol:12 -143: [12:00:57] Rep: 0 Mol:17 -143: [12:00:57] Rep: 0 Mol:16 -143: [12:00:57] Rep: 0 Mol:23 -143: [12:00:57] Rep: 0 Mol:27 -141: [12:00:57] Rep: 0 Mol:7 -141: [12:00:57] Rep: 0 Mol:21 -141: [12:00:57] Rep: 0 Mol:11 -141: [12:00:57] Rep: 0 Mol:24 -145: .[12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[12:00:57] UFFTYPER: Unrecognized hybridization for atom: 0 -145: [12:00:57] UFFTYPER: Unrecognized atom type: Cu+1 (0) -160: file testPNGMetadata_1.png gave hash 1215431680U not the expected 997629701U -108: .............[12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -159: file test4_1.png gave hash 3656546255U not the expected 3993974247U -159: Done -159: ----------------- Test 5 -143: [12:00:57] Rep: 0 Mol:31 -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -141: [12:00:57] Rep: 0 Mol:15 -145: .[12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:00:57] Rep: 0 Mol:19 -145: [12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [12:00:57] Rep: 0 Mol:20 -119: =>start test MORSE -119: =>read file -119: [12:00:57] test on : 365 molecules done -141: [12:00:57] Rep: 0 Mol:28 -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -141: [12:00:57] Rep: 0 Mol:25 -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -141: [12:00:57] Rep: 0 Mol:23 -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -141: [12:00:57] Rep: 0 Mol:27 -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -145: .[12:00:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -161: file rxn_test1_1.png gave hash 196847225U not the expected 801892091U -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -145: .[12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -145: ...[12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -108: [12:00:57] SMILES Parse Error: syntax error while parsing: --- -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] --- -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [12:00:57] dasfsadf -143: [12:00:57] Rep: 0 Mol:14 -159: file test5_1.png gave hash 3659160374U not the expected 571291290U -123/235 Test #119: testMORSE .............................. Passed 1.80 sec +143: [09:20:55] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +143: [09:20:55] cyclopropylidencyclobutane 218.879 +162: ..........[09:20:55] +162: +162: **** +162: Pre-condition Violation +162: molecule must not be None +162: Violation occurred on line 432 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp +162: Failed Expression: m +162: ---------- +162: Stacktrace: +162: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +162: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +162: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so +162: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector7 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so +162: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +162: 5# 0x00007F2C5A3A066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +162: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +162: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +162: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so +162: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +162: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +162: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +162: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +162: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +162: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +162: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 16# 0x00007F2C58FB5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 17# 0x00007F2C58FB5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 18# 0x00007F2C58FB5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 19# 0x00007F2C58FB5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 20# 0x00007F2C58FB57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +162: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +162: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +162: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +162: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +162: 26# 0x00007F2C5A39D406 in /lib/x86_64-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# 0x00000000005BEE79 in /usr/bin/python3 +162: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 +162: 31# 0x0000000000547080 in /usr/bin/python3 +162: 32# 0x00000000006AB720 in /usr/bin/python3 +162: 33# _PyObject_MakeTpCall in /usr/bin/python3 +162: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 +162: 35# 0x00000000005BEE79 in /usr/bin/python3 +162: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 +162: 37# 0x0000000000547080 in /usr/bin/python3 +162: 38# 0x00000000006AB720 in /usr/bin/python3 +162: 39# _PyObject_MakeTpCall in /usr/bin/python3 +162: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 +162: 41# 0x00000000005BEE79 in /usr/bin/python3 +162: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 +162: 43# 0x0000000000547080 in /usr/bin/python3 +162: 44# 0x00000000006AB720 in /usr/bin/python3 +162: 45# _PyObject_MakeTpCall in /usr/bin/python3 +162: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 +162: 47# 0x000000000059582E in /usr/bin/python3 +162: 48# _PyObject_MakeTpCall in /usr/bin/python3 +162: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 +162: 50# PyEval_EvalCode in /usr/bin/python3 +162: 51# 0x000000000066A861 in /usr/bin/python3 +162: 52# 0x000000000066670C in /usr/bin/python3 +162: 53# 0x000000000067F713 in /usr/bin/python3 +162: 54# 0x000000000067ECE3 in /usr/bin/python3 +162: 55# 0x000000000067EB1E in /usr/bin/python3 +162: 56# Py_RunMain in /usr/bin/python3 +162: 57# Py_BytesMain in /usr/bin/python3 +162: 58# 0x00007F2C5BB46D68 in /lib/x86_64-linux-gnu/libc.so.6 +162: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +162: 60# _start in /usr/bin/python3 +162: ---------- +162: **** +162: +143: [09:20:55] diphenylmethylidencyclobutane 79.6139 +143: [09:20:55] done +143: [09:20:55] ------------------------------------- +143: [09:20:55] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +143: [09:20:55] done +143: [09:20:55] ------------------------------------- +143: [09:20:55] Test square planar complexes +143: [09:20:55] done +143: [09:20:55] ------------------------------------- +143: [09:20:55] Test octahedral complexes +143: [09:20:55] done +145/235 Test #143: testUFFForceFieldHelpers ............... Passed 14.61 sec test 165 Start 165: FMCStest 165: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 165: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test 165: Test timeout computed to be: 1500 -141: [12:00:57] Rep: 0 Mol:31 -143: [12:00:57] Rep: 0 Mol:24 -147: [12:00:57] UFFTYPER: Unrecognized charge state for atom: 5 -143: [12:00:57] Rep: 0 Mol:28 -160: file testPNGMetadata_2.png gave hash 421119850U not the expected 1797853056U -143: [12:00:57] Rep: 0 Mol:18 -141: [12:00:57] Rep: 0 Mol:29 -147: [12:00:57] UFFTYPER: Unrecognized charge state for atom: 5 -159: file test5_2.png gave hash 3029052427U not the expected 97265124U -143: [12:00:57] Rep: 0 Mol:21 -143: [12:00:57] Rep: 0 Mol:22 -143: [12:00:57] Rep: 0 Mol:26 -159: file test5_3.png gave hash 979411683U not the expected 606188176U -143: [12:00:57] Rep: 0 Mol:25 -147: [12:00:57] UFFTYPER: Unrecognized charge state for atom: 5 -159: Done -159: ----------------- Test 6 (atom labels) -159: Done -159: ----------------- Test 7 (backgrounds) -161: file rxn_test1_2.png gave hash 1760761969U not the expected 507435337U -143: [12:00:57] Rep: 0 Mol:30 165: fopen testChEMBL_Txt(): No such file or directory -143: [12:00:57] Rep: 0 Mol:29 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory 165: fopen testChEMBL_Txt(): No such file or directory @@ -28642,255 +29778,57 @@ 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 165: ERROR: RDKit could not load input file -159: file test7_1.png gave hash 37955190U not the expected 1322246680U -159: file test7_2.png gave hash 280222352U not the expected 1499012715U -159: Done -159: ----------------- Test8: PrepareMolDrawing -159: Done -159: ----------------- Test multi-threaded drawing -159: reading molecules -141: [12:00:57] Rep: 0 Mol:14 -124/235 Test #165: FMCStest ............................... Passed 0.10 sec -145: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() +146/235 Test #165: FMCStest ............................... Passed 0.19 sec test 166 Start 166: molHashCatchTest 166: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 166: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash 166: Test timeout computed to be: 1500 -141: [12:00:57] Rep: 0 Mol:18 -125: Warning: Atom Count for residue ARG64A does not match expected count -160: [12:00:57] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:00:57] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -159: generating reference drawings -161: file rxn_test1_3.png gave hash 3097655468U not the expected 1590809137U -69: Test -69: -69: AlexRxn.mrv -69: -69: Test -69: -69: BadReactionSign.mrv -69: -69: Test -69: -69: bondArray_node.mrv -69: -69: Test -69: -69: marvin03.mrv -69: -69: Test -69: -69: marvin04.mrv -69: -69: Test -69: -69: marvin08.mrv -69: -69: Test -69: -69: marvin09.mrv -69: -69: Test -69: -69: marvin11.mrv -69: -69: Test -69: -69: marvin05.mrv -69: -69: Test -69: -69: EmptyRxn.mrv -69: -69: [12:00:57] initialization failed -160: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U -160: [12:00:57] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:00:57] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -141: [12:00:57] Rep: 0 Mol:22 -161: file rxn_test1_4.png gave hash 1178565194U not the expected 1766700542U -141: [12:00:57] Rep: 0 Mol:26 -145: ... -145: ---------------------------------------------------------------------- -145: Ran 19 tests in 0.457s -145: -145: OK -160: file testHandDrawn-1.png gave hash 2810773836U not the expected 3894611804U -141: [12:00:57] Rep: 0 Mol:30 -147: [12:00:57] UFFTYPER: Unrecognized charge state for atom: 6 -161: file rxn_test1_5.png gave hash 2486693442U not the expected 2552100594U -108: .[12:00:57] SMILES Parse Error: syntax error while parsing: mydoghasfleas -108: [12:00:57] SMILES Parse Error: check for mistakes around position 1: -108: [12:00:57] mydoghasfleas -108: [12:00:57] ^ -108: [12:00:57] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' -147: [12:00:57] UFFTYPER: Unrecognized charge state for atom: 6 -69: Test -69: -69: RxnNoCoords.mrv -69: -69: Test -69: -69: mrvValenceZero.mrv -69: -69: Test -69: -69: condition_coordinates_mpoint.mrv -69: -69: Test -69: -69: marvin01.mrv -69: -69: Test -69: -69: aspirineSynthesisWithAttributes.mrv -69: -69: Test -69: -69: marvin01.mrv -69: -69: Test -69: -69: NewChiralTest -69: -69: Test -69: -69: NewChiralTest -69: -69: Test -69: -69: NewChiralTestNoChiral -69: -69: Test -69: -69: NewChiralTestNoChiral -69: -69: Test -69: -69: NewChiralTest2 -69: -69: Test -69: -69: NewChiralTest2 -69: -69: Test -69: -69: NewChiralTest2AllChiral -69: -69: Test -69: -69: NewChiralTest2AllChiral -69: -69: Test -69: -69: Vendor839 -69: -69: Test -69: -69: DoubleBondChain -69: -69: Test -69: -69: Na_Mg_Al_OH -69: -69: Test -69: -69: Pb -69: -69: Test -69: -69: O_Mg_Si -69: -69: Test -69: -69: SquiggleBond -69: -69: Test -69: -69: BigMacrocycle -69: -69: Test -69: -69: Smiles1 -69: -148: .[12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -125/235 Test #69: testMrvToMol ........................... Passed 2.80 sec +141: [09:20:56] done +141: [09:20:56] ------------------------------------- +141: [09:20:56] Testing github 162: Incorrect SMILES after MMFF parameterization . +141: [09:20:56] done +141: [09:20:56] ------------------------------------- +141: [09:20:56] Testing github 224: crash during MMFF parameterization . +141: [09:20:56] done +141: [09:20:56] ------------------------------------- +141: [09:20:56] Testing github6728: crash due to missing stretch-bend params. +147/235 Test #141: testMMFFForceFieldHelpers .............. Passed 15.82 sec test 167 Start 167: pyMolHash 167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/Wrap/testMolHash.py" 167: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap 167: Test timeout computed to be: 1500 -160: [12:00:57] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:00:57] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -161: file rxn_test1_6.png gave hash 3683203876U not the expected 3791582903U -147: [12:00:57] UFFTYPER: Unrecognized charge state for atom: 6 -160: file testHandDrawn-2.svg gave hash 1534109833U not the expected 794717511U -160: [12:00:57] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:00:57] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -159: processing -159: launch :0 -159: launch :1 -159: launch :2 -159: launch :3 -160: file testHandDrawn-2.png gave hash 3255836690U not the expected 1443443188U -61: Test -61: -61: AtropCanon1.cxsmi -61: -61: Test -61: -61: AtropCanon2.cxsmi -61: -61: Test -61: -61: AtropCanon3.cxsmi -61: -61: Test -61: -61: BMS-986142_3d_chiral.cxsmi -61: -61: Test -61: -61: BMS-986142_3d.cxsmi -61: -61: =============================================================================== -61: All tests passed (2445 assertions in 29 test cases) -61: -126/235 Test #61: cxsmilesTest ........................... Passed 2.91 sec +166: Randomness seeded to: 4216120254 +166: =============================================================================== +166: All tests passed (363 assertions in 14 test cases) +166: +148/235 Test #166: molHashCatchTest ....................... Passed 0.23 sec test 168 Start 168: testMMPA 168: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/testMMPA 168: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA 168: Test timeout computed to be: 1500 -160: [12:00:57] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:00:57] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U -160: [12:00:57] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:00:57] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -89: [12:00:57] Explicit valence for atom # 9 N, 6, is greater than permitted -160: file testHandDrawn-3.png gave hash 1999104941U not the expected 865629432U +162: ...................... +162: ---------------------------------------------------------------------- +162: Ran 35 tests in 1.428s +162: +162: OK +162: json lasso 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.005176 seconds +168: Time elapsed 0.034848 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 168: 2: NOREF. Reference data NOT LISTED in test case. 168: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 168: 3: NOREF. Reference data NOT LISTED in test case. -160: [12:00:57] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -127/235 Test #145: pyForceFieldHelpers .................... Passed 1.34 sec 168: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 168: 4: NOREF. Reference data NOT LISTED in test case. -test 169 - Start 169: pyMMPA - -169: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap/testMMPA.py" -169: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap -169: Test timeout computed to be: 1500 168: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 168: 5: NOREF. Reference data NOT LISTED in test case. 168: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] @@ -28899,12 +29837,6 @@ 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 168: 8: NOREF. Reference data NOT LISTED in test case. -148: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -161: file rxn_test1_7.png gave hash 1361790131U not the expected 1461397406U -160: [12:00:57] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U -160: [12:00:57] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:00:57] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 168: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 168: 9: NOREF. Reference data NOT LISTED in test case. 168: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] @@ -28917,56 +29849,23 @@ 168: 13: NOREF. Reference data NOT LISTED in test case. 168: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 14: NOREF. Reference data NOT LISTED in test case. -148: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:00:57] Rep: 20 Mol:3 168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 168: 15: NOREF. Reference data NOT LISTED in test case. 168: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 168: 16: NOREF. Reference data NOT LISTED in test case. -161: file rxn_test1_7.svg gave hash 2324077060U not the expected 1831465890U 168: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. -166: Randomness seeded to: 344986525 -166: =============================================================================== -166: All tests passed (363 assertions in 14 test cases) -166: -128/235 Test #166: molHashCatchTest ....................... Passed 0.25 sec -test 170 - Start 170: testRascalMCES - -170: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES -170: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES -170: Test timeout computed to be: 1500 -161: Done -161: ----------------- Test 2: some examples that caused problems in testing -141: [12:00:57] Rep: 20 Mol:7 -141: [12:00:57] Rep: 20 Mol:11 -141: [12:00:57] Rep: 20 Mol:15 -141: [12:00:57] Rep: 20 Mol:19 -141: [12:00:57] Rep: 20 Mol:23 -154: .[12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -156: . -156: ---------------------------------------------------------------------- -156: Ran 1 test in 0.126s -156: -156: OK -156: Testing Shape Helpers wrapper -141: [12:00:57] Rep: 20 Mol:27 -141: [12:00:57] Rep: 20 Mol:31 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- -168: Time elapsed 0.006387 seconds +168: Time elapsed 0.020850 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 168: 1: PASSED. matchedRefRes = 4 -160: file testHandDrawn-4.png gave hash 1317783250U not the expected 3919767093U 168: 2: O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21, C[*:1].O=C(NCCO)[*:2] 168: 2: PASSED. matchedRefRes = 1 168: 3: O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OCC[*:2] @@ -28985,60 +29884,16 @@ 168: 9: NOREF. Reference data NOT LISTED in test case.O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 10: NULL, Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 10: PASSED. matchedRefRes = 3 -148: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() 168: 11: C([*:1])[*:2], Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 11: NOREF. Reference data NOT LISTED in test case.C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] -148: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() 168: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 12: PASSED. matchedRefRes = 8 -148: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() 168: 13: NULL, Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 13: PASSED. matchedRefRes = 9 -148: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() 168: 14: C([*:1])[*:2], Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 14: PASSED. matchedRefRes = 11 -148: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() 168: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 15: PASSED. matchedRefRes = 2 -148: [12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -161: file rxn_test2_1.png gave hash 700636031U not the expected 3551633840U -148: ..[12:00:57] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:00:57] Rep: 20 Mol:1 -141: [12:00:57] Rep: 20 Mol:5 -141: [12:00:57] Rep: 20 Mol:9 -141: [12:00:57] Rep: 20 Mol:13 -141: [12:00:57] Rep: 20 Mol:17 -141: [12:00:57] Rep: 20 Mol:0 -126: Warning: Atom Count for residue ASN39A does not match expected count -108: ....... -108: ---------------------------------------------------------------------- -108: Ran 21 tests in 2.089s -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 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] @@ -29048,41 +29903,27 @@ 168: ----------------------------------- 168: 168: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -168: Time elapsed 0.008507 seconds +168: Time elapsed 0.013272 seconds 168: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 168: 1: PASSED. matchedRefRes = 4 168: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] 168: 2: PASSED. matchedRefRes = 1 168: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2] 168: 3: PASSED. matchedRefRes = 6 -141: [12:00:57] Rep: 20 Mol:4 168: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2] 168: 4: PASSED. matchedRefRes = 13 168: 5: res= O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].O[*:2] 168: 5: PASSED. matchedRefRes = 12 -141: [12:00:58] Rep: 20 Mol:8 -141: [12:00:58] Rep: 20 Mol:12 168: 6: res= NULL,Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 168: 6: PASSED. matchedRefRes = 10 -141: [12:00:58] Rep: 20 Mol:16 -148: .[12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:00:57] Rep: 20 Mol:21 168: 7: res= O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case. -141: [12:00:58] Rep: 20 Mol:25 -141: [12:00:58] Rep: 20 Mol:29 168: 8: res= O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 9: NOREF. Reference data NOT LISTED in test case. -141: [12:00:58] Rep: 20 Mol:20 -141: [12:00:58] Rep: 20 Mol:24 -141: [12:00:58] Rep: 20 Mol:28 168: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 10: PASSED. matchedRefRes = 3 -70: [12:00:58] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -70: [12:00:58] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -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 168: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 11: NOREF. Reference data NOT LISTED in test case. 168: 12: res= C(C[*:2])[*:1],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] @@ -29091,7 +29932,6 @@ 168: 13: PASSED. matchedRefRes = 9 168: 14: res= C([*:1])[*:2],Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 14: PASSED. matchedRefRes = 11 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() 168: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 15: PASSED. matchedRefRes = 2 168: @@ -29103,27 +29943,28 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -168: Time elapsed 0.001133 seconds +168: Time elapsed 0.001265 seconds 168: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 168: 1: PASSED. matchedRefRes = 2 -161: file rxn_test2_2_1.png gave hash 766587530U not the expected 1268122583U -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() 168: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] 168: 2: PASSED. matchedRefRes = 3 168: 3: res= C([*:1])([*:2])[*:3],C1CN1[*:3].C[*:1].O=C[*:2] 168: 3: NOREF. Reference data NOT LISTED in test case. +149/235 Test #162: pyMolDraw2D ............................ Passed 2.50 sec 168: 4: res= C1CN1C([*:1])[*:2],C[*:1].O=C[*:2] 168: 4: PASSED. matchedRefRes = 4 168: 5: res= NULL,C1CN1[*:1].CC(C=O)[*:1] 168: 5: PASSED. matchedRefRes = 5 -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 +test 169 + Start 169: pyMMPA + +169: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap/testMMPA.py" +169: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap +169: Test timeout computed to be: 1500 168: 6: res= CC([*:1])[*:2],C1CN1[*:2].O=C[*:1] 168: 6: NOREF. Reference data NOT LISTED in test case. 168: 7: res= NULL,CC(N1CC1)[*:1].O=C[*:1] 168: 7: PASSED. matchedRefRes = 7 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O=C[*:3] @@ -29131,35 +29972,23 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.004841 seconds +168: Time elapsed 0.005258 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. -161: file rxn_test2_2_2.png gave hash 1252117625U not the expected 82821108U 168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 168: 2: NOREF. Reference data NOT LISTED in test case. 168: 3: res= O=C(Nc1ccccc1[*:1])[*:2],C[*:1].C[C:3]([NH+]1CCCC1)[*:2] 168: 3: NOREF. Reference data NOT LISTED in test case. 168: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 168: 4: NOREF. Reference data NOT LISTED in test case. -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 168: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 168: 5: NOREF. Reference data NOT LISTED in test case. -129/235 Test #156: pyShapeHelpers ......................... Passed 0.89 sec -test 171 - Start 171: testRascalCluster - -171: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster -171: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES -171: Test timeout computed to be: 1500 168: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 6: NOREF. Reference data NOT LISTED in test case. 168: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 168: 8: NOREF. Reference data NOT LISTED in test case. -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() 168: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 168: 9: NOREF. Reference data NOT LISTED in test case. 168: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] @@ -29170,36 +29999,27 @@ 168: 12: NOREF. Reference data NOT LISTED in test case. 168: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 13: NOREF. Reference data NOT LISTED in test case. -161: file rxn_test2_2_3.png gave hash 3797481496U not the expected 3828365604U 168: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 168: 14: NOREF. Reference data NOT LISTED in test case. -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 168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 168: 15: NOREF. Reference data NOT LISTED in test case. -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() 168: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 168: 16: NOREF. Reference data NOT LISTED in test case. 168: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. -161: file rxn_test2_2_4.png gave hash 1813989566U not the expected 1230108677U -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -161: Done -161: ----------------- Test 3: test reactant highlighting 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- 168: 168: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -168: Time elapsed 0.009511 seconds +168: Time elapsed 0.013824 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 168: 2: NOREF. Reference data NOT LISTED in test case. -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() 168: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 168: 3: NOREF. Reference data NOT LISTED in test case. 168: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1 @@ -29214,7 +30034,6 @@ 168: 8: NOREF. Reference data NOT LISTED in test case. 168: 9: res= O=C(OC[*:2])C(c1ccccc1)[*:1],O[*:1].c1ccc([*:2])cc1 168: 9: NOREF. Reference data NOT LISTED in test case. -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() 168: 10: res= O=C(OC[*:2])C([*:1])[*:3],O[*:1].c1ccc([*:2])cc1.c1ccc([*:3])cc1 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 @@ -29223,318 +30042,533 @@ 168: 12: NOREF. Reference data NOT LISTED in test case. 168: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] 168: 13: NOREF. Reference data NOT LISTED in test case. -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() 168: 14: res= C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)[*:1].O[*:2].c1ccc([*:3])cc1 168: 14: PASSED. matchedRefRes = 1 168: 15: res= OC([*:1])[*:2],O=C(OCc1ccccc1)[*:1].c1ccc([*:2])cc1 168: 15: NOREF. Reference data NOT LISTED in test case. 168: 16: res= NULL,O=C(OCc1ccccc1)C(c1ccccc1)[*:1].O[*:1] 168: 16: NOREF. Reference data NOT LISTED in test case. -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() 168: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 168: 17: NOREF. Reference data NOT LISTED in test case. -161: file rxn_test3_1.png gave hash 887759826U not the expected 4189980366U 168: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 168: 18: NOREF. Reference data NOT LISTED in test case. 168: 168: --- ALL PASSED --- 168: ----------------------------------- 168: 5 TEST CASES FAILED -130/235 Test #168: testMMPA ............................... Passed 0.25 sec +150/235 Test #168: testMMPA ............................... Passed 0.57 sec +test 170 + Start 170: testRascalMCES + +170: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES +170: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES +170: Test timeout computed to be: 1500 +167: .... +167: ---------------------------------------------------------------------- +167: Ran 4 tests in 0.062s +167: +167: OK +150: *********************************************************** +150: Testing O3AAlign +150: --------------------------------- +150: testMMFFO3A +150: +150: --------------------------------- +150: testMMFFO3A with pre-computed dmat and MolHistogram +150: +150: --------------------------------- +150: testMMFFO3A with constraints +150: +150: --------------------------------- +150: testMMFFO3A with variable weight constraints followed by local-only optimization +150: +150: --------------------------------- +150: testCrippenO3A +150: +150: --------------------------------- +150: testCrippenO3A with pre-computed dmat and MolHistogram +150: +150: --------------------------------- +150: testCrippenO3A with constraints +150: +150: --------------------------------- +150: testCrippenO3A with variable weight constraints followed by local-only optimization +150: +150: --------------------------------- +150: testMMFFO3A multithreading +150: +150: generating reference data +151/235 Test #167: pyMolHash .............................. Passed 1.24 sec +test 171 + Start 171: testRascalCluster + +171: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster +171: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES +171: Test timeout computed to be: 1500 +29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +160: file testHandDrawn-5a.svg gave hash 3327818543U not the expected 1567781555U +160: [09:20:57] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:20:57] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-5b.svg gave hash 2125846125U not the expected 66354106U +160: [09:20:57] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [09:20:57] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-5.png gave hash 2537746017U not the expected 828378555U +160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U +29: All 191 tests passed +160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U +148: [09:20:58] Molecule does not have explicit Hs. Consider calling AddHs() +160: [09:20:58] unrecognized bond typefile testGithub4238_1.png gave hash 1999044295U not the expected 2623427676U +160: file testGithub4323_1.png gave hash 1674734291U not the expected 3075787867U +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +160: file testGithub4323_3.png gave hash 4270327094U not the expected 381907253U +160: [09:20:58] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +148: [09:20:59] Molecule does not have explicit Hs. Consider calling AddHs() +163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +163: Time elapsed 0.001 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 0.322 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 0.038 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 0.014 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 0.374 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 0.156 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 0.171 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 0.162 seconds +163: +163: testSegFault() +163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +163: Time elapsed 0.013 seconds +163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +163: Time elapsed 0.017 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 0.016 seconds +163: +163: testThreshold() +163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +163: Time elapsed 0.000 seconds +163: +163: testRing1() +163: MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds +163: Time elapsed 0.537 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 1.354 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 1.576 seconds +163: +163: testAtomCompareIsotopes() +163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds +163: Time elapsed 0.000 seconds +163: +163: testAtomCompareAnyAtom() +163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +163: Time elapsed 0.000 seconds +163: +163: testAtomCompareAnyAtom() +163: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +163: Time elapsed 0.000 seconds +163: +163: testAtomCompareAnyAtom() +163: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds +163: Time elapsed 0.000 seconds +163: +163: testAtomCompareAnyAtom() +163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds +163: Time elapsed 0.000 seconds +163: +163: testJnk1LigandsDistance() +163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds +163: Time elapsed 0.049 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 +148: [09:21:00] Molecule does not have explicit Hs. Consider calling AddHs() +163: Time elapsed 0.002 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 0.041 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 0.635 seconds +163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +163: Time elapsed 0.018 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 0.206 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 0.0258 seconds. bond[0]=6 +163: STATISTICS: +163: Total Growing Steps = 1, MCS found on 1 step, for 0.0258 seconds +163: Initial Seeds = 1, Mismatched 0 +163: Inspected Seeds = 2 +163: Rejected by BestSize = 0 +163: IndividualBondExcluded = 0 +163: MatchCheck Seeds = 2 +163: MatchCalls = 2 +163: MatchFound = 1 +163: fastMatchCalls = 1 +163: fastMatchFound = 0 +163: slowMatchCalls = 2 +163: slowMatchFound = 1 +163: DupCacheFound = 0 0 matched, 0 mismatched +163: HashCache size = 1 keys +163: HashCache size = 1 entries +163: FindHashInCache = 2 +163: HashFoundInCache= 0 +163: ExactMatchCalls = 0 +163: ExactMatchFound = 0 +163: Time elapsed 0.026 seconds +163: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 +163: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 +163: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 +163: res sub = 1 size=3 +163: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +163: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 +163: res sub = 1 size=3 +163: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +163: test target = CC[C@H](F)Cl query = CCC useChirality = 0 +163: res sub = 1 size=3 +163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +163: test target = CC[C@H](F)Cl query = CCC useChirality = 1 +163: res sub = 1 size=3 +163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +163: test target = CCC(F)Cl query = CC useChirality = 0 +163: res sub = 1 size=2 +163: MCS: [#6]-[#6] 2 atoms, 1 bonds +163: test target = CCC(F)Cl query = CC useChirality = 1 +163: res sub = 1 size=2 +163: MCS: [#6]-[#6] 2 atoms, 1 bonds +163: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 +163: res sub = 1 size=4 +163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 +163: res sub = 1 size=4 +163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 +163: res sub = 0 size=0 +163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +163: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 +163: res sub = 0 size=0 +163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 +163: res sub = 0 size=0 +163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +163: test target = OC(F)CCl query = OC(F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = OC(F)CCl query = OC(F)C useChirality = 1 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 +163: res sub = 0 size=0 +163: MCS: [#9] 1 atoms, 0 bonds +163: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 +163: res sub = 1 size=4 +163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +163: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 +163: res sub = 0 size=0 +163: MCS: [#9] 1 atoms, 0 bonds +163: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 +163: res sub = 1 size=3 +163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +163: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 +163: res sub = 1 size=3 +163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 +163: res sub = 1 size=3 +163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 +163: res sub = 1 size=3 +163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +163: +163: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> +163: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 +163: res sub = 1 size=3 +163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +163: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 +163: res sub = 1 size=3 +163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +163: done +160: file testFlexiCanvas.2a.png gave hash 2907977766U not the expected 2609920321U +160: file testFlexiCanvas.2b.png gave hash 1585391483U not the expected 3615599154U +160: file testFlexiCanvas.3.svg gave hash 236661785U not the expected 3544316588U +148: [09:21:00] Molecule does not have explicit Hs. Consider calling AddHs() +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 1417438968U not the expected 2179222277U +160: file testGithub4764.sz2.png gave hash 2455997703U not the expected 444262090U +146: validating reference data +160: file testGithub4764.sz3.png gave hash 182513311U not the expected 3567162200U +148: [09:21:02] Molecule does not have explicit Hs. Consider calling AddHs() +160: file github5383_1.svg gave hash 4241964660U not the expected 1815941817U +160: file github5383_2.svg gave hash 2560846108U not the expected 0U +160: file github5383_1.png gave hash 53778753U not the expected 2893520928U +160: file acs1996_1.png gave hash 1997633690U not the expected 2329725800U +160: file acs1996_2.png gave hash 3378065352U not the expected 2996350718U +160: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U +160: [09:21:02] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. +160: file bond_highlights_8.svg gave hash 3610726614U not the expected 3119784980U +160: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U +148: [09:21:03] Molecule does not have explicit Hs. Consider calling AddHs() +150: processing +150: launch :0 +150: launch :1 +150: launch :2 +150: launch :3 +169: ......... +169: ---------------------------------------------------------------------- +169: Ran 9 tests in 6.439s +169: +169: OK +152/235 Test #169: pyMMPA ................................. Passed 7.38 sec test 172 Start 172: pyRascalMCES 172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" 172: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap 172: Test timeout computed to be: 1500 -158: . -158: ---------------------------------------------------------------------- -158: Ran 1 test in 0.029s -158: -158: OK -161: Done -161: ----------------- Test 4: some examples from SMARTS in testing -161: draw! -125: Warning: Atom Count for residue LYS80A does not match expected count -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -89: [12:00:58] Explicit valence for atom # 3 Al, 6, is greater than permitted -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -167: .... -167: ---------------------------------------------------------------------- -167: Ran 4 tests in 0.015s -167: -167: OK -161: file rxn_test4_1.png gave hash 2871076982U not the expected 2745201873U -70: [12:00:58] Empty atom list: 'M ALS 1 0 F' on line 8. -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -161: done -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -70: de_DE.UTF-8 -70: [12:00:58] ------------------------------------- -70: [12:00:58] Test multithreading Locale Switching -126: Warning: Atom Count for residue GLU53A does not match expected count -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -154: ..[12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -131/235 Test #167: pyMolHash .............................. Passed 0.41 sec +160: file AtropManyChiralsEnhanced.svg gave hash 3443464321U not the expected 2256768013U +160: file testGithub_7739_1.svg gave hash 3358510977U not the expected 2615562225U +160: file testGithub_7739_3.svg gave hash 176211825U not the expected 1037942338U +160: file testGithub_7739_4.svg gave hash 3309264286U not the expected 3549083171U +160: [09:21:05] +160: +160: **** +160: Pre-condition Violation +160: +160: Violation occurred on line 206 in file ./Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp +160: Failed Expression: atomIdx < atCds_.size() && atomIdx < atomLabels_.size() +160: ---------- +160: Stacktrace: +160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +160: 2# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::calcSymbolEllipse(unsigned int, RDGeom::Point2D&, double&, double&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeAtomHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 8# 0x000055FA99726DF5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 9# 0x000055FA99808A88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 10# 0x000055FA998095A8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 11# 0x000055FA99809A20 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 12# 0x000055FA997DB5C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 13# 0x000055FA997DB92C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 14# 0x000055FA9971F56E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 15# 0x00007FD91522ED68 in /lib/x86_64-linux-gnu/libc.so.6 +160: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +160: 17# 0x000055FA9971F5B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: ---------- +160: **** +160: +160: [09:21:05] +160: +160: **** +160: Range Error +160: idx +160: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp +160: Failed Expression: 2 < 0 +160: ---------- +160: Stacktrace: +160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +160: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 8# 0x000055FA99726562 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 9# 0x000055FA99808A88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 10# 0x000055FA998095A8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 11# 0x000055FA99809A20 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 12# 0x000055FA997DB5C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 13# 0x000055FA997DB92C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 14# 0x000055FA9971F56E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 15# 0x00007FD91522ED68 in /lib/x86_64-linux-gnu/libc.so.6 +160: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +160: 17# 0x000055FA9971F5B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: ---------- +160: **** +160: +160: [09:21:05] +160: +160: **** +160: Range Error +160: idx +160: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp +160: Failed Expression: 0 < 0 +160: ---------- +160: Stacktrace: +160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +160: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 +160: 8# 0x000055FA99726EC8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 9# 0x000055FA99808A88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 10# 0x000055FA998095A8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 11# 0x000055FA99809A20 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 12# 0x000055FA997DB5C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 13# 0x000055FA997DB92C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 14# 0x000055FA9971F56E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 15# 0x00007FD91522ED68 in /lib/x86_64-linux-gnu/libc.so.6 +160: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +160: 17# 0x000055FA9971F5B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: ---------- +160: **** +160: +160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U +163: [09:21:06] The provided InitialSeed is not an MCS and will be ignored +160: =============================================================================== +160: All tests passed (6853 assertions in 115 test cases) +160: +153/235 Test #160: moldraw2DTestCatch ..................... Passed 14.34 sec test 173 Start 173: testSynthonSpaceSubstructureSearch 173: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch 173: Test timeout computed to be: 1500 -143: [12:00:58] Rep: 100 Mol:3 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [12:00:58] Rep: 100 Mol:7 -143: [12:00:58] Rep: 100 Mol:11 -143: [12:00:58] Rep: 100 Mol:15 -143: [12:00:58] Rep: 100 Mol:19 -143: [12:00:58] Rep: 100 Mol:23 -143: [12:00:58] Rep: 100 Mol:27 -143: [12:00:58] Rep: 100 Mol:31 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -132/235 Test #158: pyMolCatalog ........................... Passed 0.97 sec +172: ..........[09:21:06] Too many matching bond pairs (1032) so can't continue. +148: .[09:21:07] Molecule does not have explicit Hs. Consider calling AddHs() +170: Randomness seeded to: 3002744838 +170: [09:21:08] Timed out after 11 seconds. +125: Warning: Atom Count for residue GLU5A does not match expected count +125: Warning: Atom Count for residue ASN39A does not match expected count +125: Warning: Atom Count for residue GLU53A does not match expected count +125: Warning: Atom Count for residue ARG64A does not match expected count +125: Warning: Atom Count for residue LYS80A does not match expected count +125: Warning: Atom Count for residue GLU150A does not match expected count +125: Warning: Atom Count for residue ASN157A does not match expected count +125: =============================================================================== +125: All tests passed (515 assertions in 10 test cases) +125: +154/235 Test #125: descriptorsTestCatch ................... Passed 32.93 sec test 174 Start 174: testCIPLabeler 174: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 174: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler 174: Test timeout computed to be: 1500 -161: file rxn_test4_2.png gave hash 424710428U not the expected 3094925886U -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[12:00:58] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -154: [12:00:58] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' -154: ... -154: ---------------------------------------------------------------------- -154: Ran 9 tests in 0.349s -154: -154: OK -133/235 Test #108: pyFilterCatalog ........................ Passed 2.85 sec +174: Randomness seeded to: 3194890023 +174: [09:21:08] non kekulizable aromatic bond being treated as bond order 1 +174: [09:21:08] non kekulizable aromatic bond being treated as bond order 1 +174: [09:21:08] non kekulizable aromatic bond being treated as bond order 1 +174: [09:21:08] non kekulizable aromatic bond being treated as bond order 1 +174: [09:21:08] non kekulizable aromatic bond being treated as bond order 1 +174: [09:21:08] non kekulizable aromatic bond being treated as bond order 1 +173: Randomness seeded to: 2329723200 +173: [09:21:09] Writing the enumerated file may take quite some time and result in a large file. +174: [09:21:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +174: [09:21:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +146: processing +146: launch :0 +146: launch :1 +146: launch :2 +146: launch :3 +174: =============================================================================== +174: All tests passed (6577 assertions in 19 test cases) +174: +155/235 Test #174: testCIPLabeler ......................... Passed 0.77 sec test 175 Start 175: pyCIPLabelsWrapTest 175: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" 175: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 175: Test timeout computed to be: 1500 -89: [12:00:58] Explicit valence for atom # 4 Al, 6, is greater than permitted -141: [12:00:58] Rep: 40 Mol:3 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:00:58] Rep: 40 Mol:7 -141: [12:00:58] Rep: 40 Mol:11 -141: [12:00:58] Rep: 40 Mol:15 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:00:58] Rep: 40 Mol:19 -141: [12:00:58] Rep: 40 Mol:23 -141: [12:00:58] Rep: 40 Mol:27 -141: [12:00:58] Rep: 40 Mol:31 -161: Done -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -134/235 Test #161: moldraw2DRxnTest1 ...................... Passed 0.86 sec +175: .... +175: ---------------------------------------------------------------------- +175: Ran 4 tests in 0.049s +175: +175: OK +156/235 Test #175: pyCIPLabelsWrapTest .................... Passed 1.04 sec test 176 Start 176: pyCIPLabelsValidation 176: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 176: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 176: Test timeout computed to be: 1500 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -89: [12:00:58] Explicit valence for atom # 10 Si, 6, is greater than permitted -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -174: Randomness seeded to: 3295035854 -174: [12:00:58] non kekulizable aromatic bond being treated as bond order 1 -174: [12:00:58] non kekulizable aromatic bond being treated as bond order 1 -174: [12:00:58] non kekulizable aromatic bond being treated as bond order 1 -174: [12:00:58] non kekulizable aromatic bond being treated as bond order 1 -174: [12:00:58] non kekulizable aromatic bond being treated as bond order 1 -174: [12:00:58] non kekulizable aromatic bond being treated as bond order 1 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -70: [12:00:58] Test multithreading (Done) -70: [12:00:58] ------------------------------------- -162: ...[12:00:58] Font file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -162: [12:00:58] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -70: *************************************** -70: *************************************** -70: [12:00:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [12:00:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -126: Warning: Atom Count for residue ARG64A does not match expected count -141: [12:00:58] Rep: 20 Mol:2 -141: [12:00:58] Rep: 20 Mol:6 -141: [12:00:58] Rep: 20 Mol:10 -141: [12:00:58] Rep: 20 Mol:14 -141: [12:00:58] Rep: 20 Mol:18 -162: ..........[12:00:58] -162: -162: **** -162: Pre-condition Violation -162: molecule must not be None -162: Violation occurred on line 432 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp -162: Failed Expression: m -162: ---------- -162: Stacktrace: -162: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -162: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -162: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so -162: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector7 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so -162: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -162: 5# 0x00007F73974B266C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -162: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -162: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -162: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so -162: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -162: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -162: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -162: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -162: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -162: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -162: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 16# 0x00007F73959B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 17# 0x00007F73959B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 18# 0x00007F73959B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 19# 0x00007F73959B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 20# 0x00007F73959B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -162: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -162: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -162: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -162: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -162: 26# 0x00007F73974AF406 in /lib/x86_64-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# 0x00000000005BEE79 in /usr/bin/python3 -162: 30# _PyEval_EvalFrameDefault in /usr/bin/python3 -162: 31# 0x0000000000547080 in /usr/bin/python3 -162: 32# 0x00000000006AB720 in /usr/bin/python3 -162: 33# _PyObject_MakeTpCall in /usr/bin/python3 -162: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 -162: 35# 0x00000000005BEE79 in /usr/bin/python3 -162: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 -162: 37# 0x0000000000547080 in /usr/bin/python3 -162: 38# 0x00000000006AB720 in /usr/bin/python3 -162: 39# _PyObject_MakeTpCall in /usr/bin/python3 -162: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 -162: 41# 0x00000000005BEE79 in /usr/bin/python3 -162: 42# _PyEval_EvalFrameDefault in /usr/bin/python3 -162: 43# 0x0000000000547080 in /usr/bin/python3 -162: 44# 0x00000000006AB720 in /usr/bin/python3 -162: 45# _PyObject_MakeTpCall in /usr/bin/python3 -162: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 -162: 47# 0x000000000059582E in /usr/bin/python3 -162: 48# _PyObject_MakeTpCall in /usr/bin/python3 -162: 49# _PyEval_EvalFrameDefault in /usr/bin/python3 -162: 50# PyEval_EvalCode in /usr/bin/python3 -162: 51# 0x000000000066A861 in /usr/bin/python3 -162: 52# 0x000000000066670C in /usr/bin/python3 -162: 53# 0x000000000067F713 in /usr/bin/python3 -162: 54# 0x000000000067ECE3 in /usr/bin/python3 -162: 55# 0x000000000067EB1E in /usr/bin/python3 -162: 56# Py_RunMain in /usr/bin/python3 -162: 57# Py_BytesMain in /usr/bin/python3 -162: 58# 0x00007F73986BFD68 in /lib/x86_64-linux-gnu/libc.so.6 -162: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -162: 60# _start in /usr/bin/python3 -162: ---------- -70: [12:00:58] bond with order 0 found on line 7. This is not part of the MDL specification. -162: **** -162: -141: [12:00:58] Rep: 20 Mol:22 -141: [12:00:58] Rep: 20 Mol:26 -141: [12:00:58] Rep: 20 Mol:30 -130: [12:00:58] done -130: [12:00:58] ------------------------------------- -130: [12:00:58] Test GitHub Issue #6958 -130: [12:00:58] DEPRECATION WARNING: please use AtomPairGenerator -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -135/235 Test #130: testFingerprintGenerators .............. Passed 2.39 sec +172: .... +172: ---------------------------------------------------------------------- +172: Ran 14 tests in 4.942s +172: +172: OK +157/235 Test #172: pyRascalMCES ........................... Passed 6.94 sec test 177 Start 177: deprotectTest 177: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 177: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect 177: Test timeout computed to be: 1500 -70: [12:00:58] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -141: [12:00:58] Rep: 40 Mol:0 -70: [12:00:58] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -70: [12:00:58] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:00:58] Rep: 40 Mol:4 -141: [12:00:58] Rep: 40 Mol:8 -141: [12:00:58] Rep: 40 Mol:12 -141: [12:00:58] Rep: 40 Mol:16 -141: [12:00:58] Rep: 40 Mol:20 -141: [12:00:58] Rep: 40 Mol:24 -141: [12:00:58] Rep: 40 Mol:1 -141: [12:00:58] Rep: 40 Mol:5 -141: [12:00:58] Rep: 40 Mol:9 -141: [12:00:58] Rep: 40 Mol:13 -141: [12:00:58] Rep: 40 Mol:17 -141: [12:00:58] Rep: 40 Mol:28 -141: [12:00:58] Rep: 40 Mol:21 -141: [12:00:58] Rep: 40 Mol:25 -141: [12:00:58] Rep: 40 Mol:29 -136/235 Test #154: pyChemicalFeatures ..................... Passed 1.35 sec +177: Randomness seeded to: 3930930490 +177: =============================================================================== +177: All tests passed (111 assertions in 3 test cases) +177: +158/235 Test #177: deprotectTest .......................... Passed 0.33 sec test 178 Start 178: pyDeprotect 178: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/Wrap/rough_test.py" 178: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap 178: Test timeout computed to be: 1500 -141: [12:00:58] Rep: 60 Mol:3 -174: [12:00:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -174: [12:00:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -141: [12:00:58] Rep: 60 Mol:7 -70: generating smiles -70: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -70: converting back -141: [12:00:58] Rep: 60 Mol:11 -141: [12:00:58] Rep: 60 Mol:15 -141: [12:00:58] Rep: 60 Mol:19 -141: [12:00:58] Rep: 60 Mol:23 -141: [12:00:58] Rep: 60 Mol:27 -141: [12:00:58] Rep: 60 Mol:31 -70: check isomorphism -117: =>start test morse custom -117: [12:00:58] test on : 365 molecules done -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -162: ...................... -162: ---------------------------------------------------------------------- -162: Ran 35 tests in 0.244s -162: -162: OK -162: json lasso -174: =============================================================================== -174: All tests passed (6577 assertions in 19 test cases) -174: -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -137/235 Test #174: testCIPLabeler ......................... Passed 0.35 sec +95: 0,0 0 +95: 0,1 0 +95: 1,0 0 +95: 1,1 0 +95: 2,0 0 +95: 2,1 0 +159/235 Test #95: testEnumeration ........................ Passed 44.34 sec test 179 Start 179: testReducedGraphs 179: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs 179: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs 179: Test timeout computed to be: 1500 -126: Warning: Atom Count for residue LYS80A does not match expected count -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -89: [12:00:58] Explicit valence for atom # 2 O, 4, is greater than permitted -175: .... -175: ---------------------------------------------------------------------- -175: Ran 4 tests in 0.020s -175: -175: OK -172: ..........[12:00:58] Too many matching bond pairs (1032) so can't continue. 179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 179: 179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0.3, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] @@ -29543,20 +30577,6 @@ 179: 179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.3, 1.3, 0.6, 1, 0.6, 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, 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, ] 179: -177: Randomness seeded to: 2654984791 -177: =============================================================================== -177: All tests passed (111 assertions in 3 test cases) -177: -89: [12:00:58] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [12:00:58] Explicit valence for atom # 3 Be, 4, is greater than permitted -138/235 Test #177: deprotectTest .......................... Passed 0.23 sec -test 180 - Start 180: pyReducedGraphs - -180: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" -180: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap -180: Test timeout computed to be: 1500 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() 179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.6, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1.3, 1.3, 0.6, 1, 0.6, 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, 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, ] 179: 179: 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, ] @@ -29567,142 +30587,16 @@ 179: 179: 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, ] 179: -139/235 Test #175: pyCIPLabelsWrapTest .................... Passed 0.45 sec -140/235 Test #179: testReducedGraphs ...................... Passed 0.12 sec -test 181 - Start 181: trajectoryTest - -181: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest -181: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory -181: Test timeout computed to be: 1500 -test 182 - Start 182: substructLibraryTest - -182: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest -182: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary -182: Test timeout computed to be: 1500 -141/235 Test #162: pyMolDraw2D ............................ Passed 1.28 sec -89: [12:00:58] Explicit valence for atom # 27 P, 6, is greater than permitted -test 183 - Start 183: substructLibraryCatchTest - -183: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest -183: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary -183: Test timeout computed to be: 1500 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:00:58] Rep: 80 Mol:3 -141: [12:00:58] Rep: 80 Mol:7 -141: [12:00:58] Rep: 60 Mol:1 -141: [12:00:58] Rep: 60 Mol:5 -141: [12:00:58] Rep: 60 Mol:9 -141: [12:00:58] Rep: 80 Mol:11 -141: [12:00:58] Rep: 80 Mol:15 -141: [12:00:58] Rep: 80 Mol:19 -141: [12:00:58] Rep: 80 Mol:23 -141: [12:00:58] Rep: 80 Mol:27 -141: [12:00:58] Rep: 80 Mol:31 -141: [12:00:58] Rep: 60 Mol:13 -141: [12:00:58] Rep: 60 Mol:17 -141: [12:00:58] Rep: 60 Mol:21 -141: [12:00:58] Rep: 60 Mol:25 -89: =============================================================================== -89: All tests passed (21562 assertions in 3 test cases) -89: -142/235 Test #89: multithreadedSupplierCatchTest ......... Passed 3.58 sec -test 184 - Start 184: pySubstructLibrary +160/235 Test #179: testReducedGraphs ...................... Passed 0.23 sec +test 180 + Start 180: pyReducedGraphs -184: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" -184: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap -184: Test timeout computed to be: 1500 -141: [12:00:58] Rep: 60 Mol:29 -143: [12:00:58] Rep: 100 Mol:0 -143: [12:00:58] Rep: 100 Mol:4 -143: [12:00:58] Rep: 100 Mol:8 -143: [12:00:58] Rep: 100 Mol:12 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [12:00:58] Rep: 100 Mol:16 -143: [12:00:58] Rep: 100 Mol:20 -143: [12:00:58] Rep: 100 Mol:24 -143: [12:00:58] Rep: 100 Mol:28 -182: [12:00:58] ------------------------------------- -182: [12:00:58] Test1 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:00:58] Rep: 60 Mol:0 -141: [12:00:58] Rep: 60 Mol:4 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:00:58] Rep: 60 Mol:8 -141: [12:00:58] Rep: 60 Mol:12 -141: [12:00:58] Rep: 60 Mol:16 -141: [12:00:58] Rep: 60 Mol:20 -141: [12:00:58] Rep: 60 Mol:24 -143: [12:00:58] Rep: 100 Mol:1 -143: [12:00:58] Rep: 100 Mol:5 -143: [12:00:58] Rep: 100 Mol:9 -143: [12:00:58] Rep: 100 Mol:13 -143: [12:00:58] Rep: 100 Mol:17 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -143: [12:00:58] Rep: 100 Mol:21 -143: [12:00:58] Rep: 100 Mol:25 -141: [12:00:58] Rep: 60 Mol:28 -141: [12:00:58] Rep: 40 Mol:2 -143: [12:00:58] Rep: 100 Mol:29 -141: [12:00:58] Rep: 40 Mol:6 -141: [12:00:58] Rep: 40 Mol:10 -141: [12:00:58] Rep: 40 Mol:14 -141: [12:00:58] Rep: 40 Mol:18 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: [12:00:58] Rep: 40 Mol:22 -141: [12:00:58] Rep: 40 Mol:26 -141: [12:00:58] Rep: 40 Mol:30 -148: [12:00:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:59] Molecule does not have explicit Hs. Consider calling AddHs() -41: [12:00:59] done: 500000 -41: [12:00:59] Done -148: [12:00:59] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:00:59] Molecule does not have explicit Hs. Consider calling AddHs() -41: [12:00:59] Testing hanoi with a functor. -148: [12:00:59] Molecule does not have explicit Hs. Consider calling AddHs() -41: [12:00:59] Done -41: [12:00:59] Testing basic partition refinement. -41: [12:00:59] Done -41: [12:00:59] Testing partition refinement with neighbors. -41: [12:00:59] Done -41: [12:00:59] testing canonicalization via tie breaking. -41: [12:00:59] Done -41: [12:00:59] testing canonicalization using the wrapper. -141: [12:00:59] Rep: 80 Mol:1 -141: [12:00:59] Rep: 80 Mol:5 -141: [12:00:59] Rep: 80 Mol:9 -141: [12:00:59] Rep: 80 Mol:13 -141: [12:00:59] Rep: 80 Mol:17 -141: [12:00:59] Rep: 80 Mol:21 -141: [12:00:59] Rep: 80 Mol:25 -141: [12:00:59] Rep: 80 Mol:29 -41: [12:00:59] Done -41: [12:00:59] testing some specific ordering problems -41: [12:00:59] Finished -41: [12:00:59] testing chiral invariants. -41: [12:00:59] Finished -41: [12:00:59] testing unique ranks in w.r.t. renumbering. -143: [12:00:59] Rep: 100 Mol:2 -143: [12:00:59] Rep: 100 Mol:6 -143: [12:00:59] Rep: 100 Mol:10 -148: [12:00:59] Molecule does not have explicit Hs. Consider calling AddHs() -143: [12:00:59] Rep: 100 Mol:14 -143: [12:00:59] Rep: 100 Mol:18 -143: [12:00:59] Rep: 100 Mol:22 -143: [12:00:59] Rep: 100 Mol:26 -143: [12:00:59] Rep: 100 Mol:30 -41: [12:00:59] Finished -41: [12:00:59] testing mol fragments. -41: [12:00:59] Finished -41: [12:00:59] testing protein round-tripping. -148: .[12:00:59] Molecule does not have explicit Hs. Consider calling AddHs() +180: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" +180: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap +180: Test timeout computed to be: 1500 178: ..... 178: ---------------------------------------------------------------------- -178: Ran 5 tests in 0.179s +178: Ran 5 tests in 0.111s 178: 178: OK 178: Testing tert-butyldimethylsilyl @@ -29755,207 +30649,434 @@ 178: Testing acetamide 178: Testing carbobenzyloxy 178: Testing Acetal/Ketal +161/235 Test #178: pyDeprotect ............................ Passed 1.74 sec +test 181 + Start 181: trajectoryTest + +181: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest +181: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory +181: Test timeout computed to be: 1500 +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 180: ..... 180: ---------------------------------------------------------------------- -180: Ran 5 tests in 0.059s +180: Ran 5 tests in 0.039s 180: 180: OK -29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -41: [12:01:00] Finished -41: [12:01:00] testing stability w.r.t. renumbering. -143/235 Test #180: pyReducedGraphs ........................ Passed 1.63 sec +126: Warning: Atom Count for residue GLU150A does not match expected count +126: Warning: Atom Count for residue ASN157A does not match expected count +126: .[09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: .[09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: ..[09:21:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:21:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:21:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:21:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:21:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:21:13] DEPRECATION WARNING: please use AtomPairGenerator +126: .[09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ...[09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: [09:21:13] DEPRECATION WARNING: please use MorganGenerator +126: ....[09:21:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:21:13] DEPRECATION WARNING: please use AtomPairGenerator +126: ....[09:21:13] DEPRECATION WARNING: please use AtomPairGenerator +126: [09:21:13] DEPRECATION WARNING: please use AtomPairGenerator +126: .[09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [09:21:13] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ... +126: ---------------------------------------------------------------------- +126: Ran 31 tests in 36.238s +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 +162/235 Test #180: pyReducedGraphs ........................ Passed 0.95 sec +test 182 + Start 182: substructLibraryTest + +182: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest +182: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary +182: Test timeout computed to be: 1500 +182: [09:21:13] ------------------------------------- +182: [09:21:13] Test1 +163/235 Test #126: pyMolDescriptors ....................... Passed 37.39 sec +test 183 + Start 183: substructLibraryCatchTest + +183: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest +183: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary +183: Test timeout computed to be: 1500 +171: Randomness seeded to: 2836107370 +171: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/data/chembl_1907596.smi +182: [09:21:14] done +182: [09:21:14] ------------------------------------- +182: [09:21:14] Test2 +164/235 Test #181: trajectoryTest ......................... Passed 1.86 sec +test 184 + Start 184: pySubstructLibrary + +184: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" +184: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap +184: Test timeout computed to be: 1500 +182: [09:21:15] done +182: [09:21:15] ------------------------------------- +182: [09:21:15] Test3 (stereo options) +182: [09:21:15] Done (stereo options) +182: [09:21:15] ------------------------------------- +182: [09:21:15] Test4 (trusted smiles) +182: [09:21:15] Done (trusted smiles) +182: [09:21:15] ------------------------------------- +182: [09:21:15] Testing C++ docs +182: [09:21:15] Done (C++ doc tests) +182: [09:21:15] ------------------------------------- +182: [09:21:15] Testing C++ ring query: PatternHolder +182: [09:21:15] Done (C++ ring query tests) +182: [09:21:15] ------------------------------------- +182: [09:21:15] Testing C++ ring query: TautomerPatternHolder +182: [09:21:15] Done (C++ ring query tests) +182: [09:21:15] ------------------------------------- +182: [09:21:15] Add Patterns +183: Randomness seeded to: 2320404929 +183: =============================================================================== +183: All tests passed (171 assertions in 5 test cases) +183: +165/235 Test #183: substructLibraryCatchTest .............. Passed 2.02 sec test 185 Start 185: testRGroupDecomp 185: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 185: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 185: Test timeout computed to be: 1500 -141: [12:01:00] Rep: 60 Mol:2 -141: [12:01:00] Rep: 60 Mol:6 -141: [12:01:00] Rep: 60 Mol:10 -141: [12:01:00] Rep: 60 Mol:14 -141: [12:01:00] Rep: 60 Mol:18 -141: [12:01:00] Rep: 60 Mol:22 -141: [12:01:00] Rep: 60 Mol:26 -141: [12:01:00] Rep: 60 Mol:30 -41: [12:01:00] Finished -41: [12:01:00] testing smiles round-tripping. -117: =>start test AUTOCORR3D custom -117: [12:01:00] test on : 365 molecules done -41: [12:01:00] Finished -41: [12:01:00] testing github #1567: Non-canonical result from MolFragmentToSmiles() -41: [12:01:00] Finished -144/235 Test #41: hanoiTest .............................. Passed 5.70 sec +164: ........................................[09:21:15] The provided InitialSeed is not an MCS and will be ignored +164: [09:21:15] The provided InitialSeed is not an MCS and will be ignored +164: [09:21:15] The provided InitialSeed is not an MCS and will be ignored +164: .[09:21:16] The provided InitialSeed is not an MCS and will be ignored +164: [09:21:16] The provided InitialSeed is not an MCS and will be ignored +164: [09:21:16] The provided InitialSeed is not an MCS and will be ignored +164: .[09:21:16] The provided InitialSeed is not an MCS and will be ignored +164: [09:21:16] The provided InitialSeed is not an MCS and will be ignored +164: [09:21:16] The provided InitialSeed is not an MCS and will be ignored +164: .[09:21:16] The provided InitialSeed is not an MCS and will be ignored +164: [09:21:16] The provided InitialSeed is not an MCS and will be ignored +164: [09:21:16] The provided InitialSeed is not an MCS and will be ignored +185: [09:21:16] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +185: [09:21:16] WARNING: not removing hydrogen atom with dummy atom neighbors +164: ................. +164: ---------------------------------------------------------------------- +164: Ran 60 tests in 20.151s +164: +164: OK +166/235 Test #164: pyFMCS ................................. Passed 21.48 sec test 186 Start 186: testRGroupDecompInternals 186: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 186: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 186: Test timeout computed to be: 1500 -98: . -98: ---------------------------------------------------------------------- -98: Ran 11 tests in 4.719s -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 0.17806410789489746 seconds -98: Skipped 10000000 in 1.8532090187072754 seconds -98: Skipped 10000000 in 1.9986915588378906 seconds -141: [12:01:00] Rep: 80 Mol:0 -141: [12:01:00] Rep: 80 Mol:4 -141: [12:01:00] Rep: 80 Mol:8 -141: [12:01:00] Rep: 80 Mol:12 -141: [12:01:00] Rep: 80 Mol:16 -141: [12:01:00] Rep: 80 Mol:20 -141: [12:01:00] Rep: 80 Mol:24 -141: [12:01:00] Rep: 80 Mol:28 -29: All 191 tests passed -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -145/235 Test #98: pyChemReactionEnumerations ............. Passed 5.28 sec -146/235 Test #186: testRGroupDecompInternals .............. Passed 0.08 sec +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [09:21:17] WARNING: not removing hydrogen atom with dummy atom neighbors +167/235 Test #186: testRGroupDecompInternals .............. Passed 0.41 sec test 187 Start 187: rgroupCatchTests 187: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 187: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 187: 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 4245589364U not the expected 675908852U +159: file test3_2.png gave hash 3367333300U not the expected 2452584093U +159: file test3_3.png gave hash 2996581333U not the expected 1907006999U +159: file test3_4.png gave hash 3977004105U not the expected 2305641511U +173: [09:21:18] Building the fingerprints may take some time. +52: Randomness seeded to: 2292479403 +52: =============================================================================== +52: All tests passed (14835 assertions in 14 test cases) +52: +168/235 Test #52: canonTestsCatch ........................ Passed 53.21 sec test 188 Start 188: pyRGroupDecomposition 188: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 188: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 188: Test timeout computed to be: 1500 -147/235 Test #178: pyDeprotect ............................ Passed 2.15 sec +159: file test3_5.png gave hash 3967750587U not the expected 3842605920U +159: file test3_6.png gave hash 691593501U not the expected 662622011U +159: file test3_7.png gave hash 1614455692U not the expected 469729412U +159: Done +159: ----------------- Test Github774: upside-down drawings +159: file test774_1.png gave hash 383494043U not the expected 428322245U +159: file test774_2.png gave hash 2504225659U not the expected 4095288521U +159: Done +159: ----------------- Test 9 (molecule legends) +159: file test9_1.svg gave hash 923579170U not the expected 1484349178U +159: Done +159: ----------------- Test Github852: Lines used to wedge bonds are too thick +159: file test852_1.png gave hash 2064209894U not the expected 271517011U +159: file test852_2.png gave hash 869339719U not the expected 967452082U +159: ---------------- +159: ---------------- +159: ---------------- +159: ---------------- +159: Done +159: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right +159: file test860_1.png gave hash 1884717540U not the expected 2835587240U +159: file test860_2.png gave hash 3946798084U not the expected 1116015475U +159: file test860_3.png gave hash 2321130724U not the expected 1872467868U +159: Done +159: ----------------- Test Github #910: ugly coordinates generated for peptide chains +159: Done +159: ----------------- Test Github #932: mistake in SVG for wedged bonds +159: Done +159: ----------------- Test Github #953: default color should not be cyan +159: Done +159: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly +159: Done +159: ----------------- Test Deuterium, Tritium +159: Done +159: ----------------- Test crossed bonds +159: Done +159: ----------------- Testing drawing a second molecule +159: Done +159: ----------------- Testing drawing a grid of molecules +159: Done +159: ----------------- Testing drawMolecules +159: file test12_1.svg gave hash 76786371U not the expected 826649652U +187: Randomness seeded to: 4203353059 +187: =============================================================================== +187: All tests passed (1475 assertions in 14 test cases) +187: +169/235 Test #187: rgroupCatchTests ....................... Passed 2.73 sec test 189 Start 189: molInterchangeTest1 189: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 189: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 189: Test timeout computed to be: 1500 -189: [12:01:00] test1: basics -141: [12:01:00] Rep: 80 Mol:2 -173: Randomness seeded to: 2951161614 -173: [12:01:00] Writing the enumerated file may take quite some time and result in a large file. -189: [12:01:00] done -189: [12:01:00] test2: basic writing -70: [12:01:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [12:01:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [12:01:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [12:01:00] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +189: [09:21:20] test1: basics +189: [09:21:20] done +189: [09:21:20] test2: basic writing 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[0,0]}]}]} 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","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]]}]}]} 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","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]]}]}]} -189: [12:01:00] done -189: [12:01:00] test3: writing conformers +189: [09:21:20] done +189: [09:21:20] test3: writing conformers 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1988,-0.0452],[-0.3332,0.4556],[0.166,1.322],[0.5332,-0.0438],[-2.0652,0.4542],[-0.834,1.3212]]},{"dim":3,"coords":[[0.9554,-0.3743,-0.4679],[-0.3616,-0.1311,-0.0795],[-0.5097,1.6256,0.1706],[-0.5779,-0.792,1.1042],[1.5277,0.1064,0.1628],[-1.0339,-0.4346,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.6","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} -189: [12:01:00] done -189: [12:01:00] test4: writing properties +189: [09:21:20] done +189: [09:21:20] test4: writing properties 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"properties":{"foo_string":"bar","foo_int":1,"foo_double":1.2},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[0,0]}]}]} -189: [12:01:00] done -189: [12:01:00] test5: writing partial charges +189: [09:21:20] done +189: [09:21:20] test5: writing partial charges 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"z":8,"impHs":1}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.6","values":[0.5,-0.5]}]}]} -189: [12:01:00] testing parse options -141: [12:01:00] Rep: 80 Mol:6 -189: [12:01:00] done -189: [12:01:00] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +189: [09:21:20] testing parse options +189: [09:21:20] done +189: [09:21:20] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":2},{"impHs":2},{"impHs":2},{"z":8},{"impHs":1,"stereo":"cw"},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -189: [12:01:00] done -189: [12:01:00] testing 'either' stereochemistry -189: [12:01:00] done -141: [12:01:00] Rep: 80 Mol:10 -141: [12:01:00] Rep: 80 Mol:14 -141: [12:01:00] Rep: 80 Mol:18 -148/235 Test #189: molInterchangeTest1 .................... Passed 0.07 sec +189: [09:21:20] done +189: [09:21:20] testing 'either' stereochemistry +189: [09:21:20] done +170/235 Test #189: molInterchangeTest1 .................... Passed 0.17 sec test 190 Start 190: molInterchangeCatchTest 190: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 190: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 190: Test timeout computed to be: 1500 -70: [12:01:00] deprecated group abbreviation ignored on line 24 -70: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -70: [12:01:00] -70: -70: **** -70: Post-condition Violation -70: Element 'Mv' not found -70: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -70: Failed Expression: anum > -1 -70: ---------- -70: Stacktrace: -70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 3# 0x00007F77AB6C8391 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 4# 0x00007F77AB6D1CFA in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 5# 0x00007F77AB6D207D in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 9# 0x0000558932464CF5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 10# 0x00005589324CB4F2 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 11# 0x000055893244B9E3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 12# 0x00007F77AAC33D68 in /lib/x86_64-linux-gnu/libc.so.6 -70: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -70: 14# 0x000055893244BB11 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: ---------- -70: **** -70: -141: [12:01:00] Rep: 80 Mol:22 -141: [12:01:00] Rep: 80 Mol:26 -141: [12:01:00] Rep: 80 Mol:30 -149/235 Test #181: trajectoryTest ......................... Passed 2.03 sec +159: Done +159: ----------------- Test JSON Configuration +159: Done +159: ----------------- Testing github 1090: escape html characters in SVG output +159: Done +159: ----------------- Testing github 1035: overflow bug in SVG color generation +159: Done +159: ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes +159: Done +159: ----------------- Testing github 1322: add custom atom labels +159: Done +159: ----------------- Testing use of a black & white palette +159: Done +159: ----------------- Testing use of continuous highlighting with drawMolecules +159: Done +159: ----------------- Test 17 - Testing maximum font size +159: Done +159: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list +159: Done +159: ----------------- Testing use of fixed scales for drawing. +190: Randomness seeded to: 395734615 +190: [09:21:20] unrecognized bond type 12 set to zero while writing +190: [09:21:20] unrecognized bond type 0 set to zero while writing +190: =============================================================================== +190: All tests passed (125 assertions in 7 test cases) +190: +171/235 Test #190: molInterchangeCatchTest ................ Passed 0.29 sec test 191 Start 191: pyMolInterchange 191: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 191: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 191: Test timeout computed to be: 1500 -190: Randomness seeded to: 1186578214 -190: [12:01:00] unrecognized bond type 12 set to zero while writing -190: [12:01:00] unrecognized bond type 0 set to zero while writing -190: =============================================================================== -190: All tests passed (125 assertions in 7 test cases) -190: -150/235 Test #190: molInterchangeCatchTest ................ Passed 0.09 sec +159: Done +159: ----------------- Testing rotation of 2D drawing. +159: Done +159: ----------------- Testing inclusion of molecule metadata +159: Done +159: ----------------- Testing Github2063: Drawing racemic bond stereo as crossed bonds should be the default +159: Done +159: ----------------- Testing Github2151: MolDraw2D: line width should be controlled by MolDrawOptions +159: file testGithub2151_1.svg gave hash 3620378781U not the expected 4119581143U +159: file testGithub2151_2.svg gave hash 3896781930U not the expected 425960913U +159: Done +159: ----------------- Testing testGithub2762: MolDraw2D: HCl and ethane should be drawn +159: Done +159: ----------------- Testing testGithub2931: multi-coloured molecule highlights. +159: file testGithub2931_1.svg gave hash 811930351U not the expected 3635831631U +159: file testGithub2931_3.svg gave hash 1986517899U not the expected 2885834646U +159: Done +159: ----------------- Testing annotation of 2D Drawing. +159: file test20_1.png gave hash 1526801019U not the expected 200877868U +159: file test20_2.png gave hash 1568015929U not the expected 1651164846U +159: file test20_3.png gave hash 2265759724U not the expected 1463603076U +159: file test20_4.png gave hash 960727959U not the expected 1714613205U +159: Done +159: ----------------- Test 21 - different font +159: Done +159: ----------------- Test 22 - draw explicit methyls. +159: Done +159: ----------------- Testing drawing of legends. +159: Done +159: ----------------- Test Github 3305 - change and scale line widths. +159: file testGithub3305_1.png gave hash 4250074512U not the expected 3303791649U +185: iterative +159: file testGithub3305_2.png gave hash 2438913291U not the expected 4003267433U +159: file testGithub3305_3.png gave hash 1680056767U not the expected 273338209U +159: file testGithub3305_4.png gave hash 3967750587U not the expected 3842605920U +159: file testGithub3305_5.png gave hash 2464937348U not the expected 151279576U +159: file testGithub3305_5.svg gave hash 3310590632U not the expected 1335449325U +159: file testGithub3305_6.png gave hash 1984494277U not the expected 613418460U +191: .. +191: ---------------------------------------------------------------------- +191: Ran 2 tests in 0.051s +191: +191: OK +159: file testGithub3305_7.png gave hash 2361405774U not the expected 2835747678U +159: Done +159: ----------------- Test Github 3391 - maxFontSize interacting badly with DrawMolecules. +159: Done +159: ----------------- Test Github 4156 - bad scale for radicals in grid +159: Done +159: ----------------- Test JSON atomColourPalette +159: Done +159: ----------------- Test draw aromatic OR queries +159: Done +159: ----------------- Test AND queries +159: Done +172/235 Test #159: moldraw2DTest1 ......................... Passed 30.91 sec test 192 Start 192: testSLNParse 192: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 192: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse 192: Test timeout computed to be: 1500 -148: [12:01:00] Molecule does not have explicit Hs. Consider calling AddHs() -147: [12:01:00] UFFTYPER: Warning: hybridization set to SP3 for atom 6 192: Atoms: 192: 0 6 C chg: 1 deg: 5 exp: N/A imp: 0 hyb: 192: 1 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: @@ -29969,42 +31090,42 @@ 192: 2 0->3 order: 1 192: 3 0->4 order: 1 192: 4 0->5 order: 1 -192: [12:01:00] SLN Parse Error: syntax error while parsing: CH4[I=13] -192: [12:01:00] Failed parsing SLN 'CH4[I=13]' -192: [12:01:00] SLN Parser error: Atom ID 1 appears *after* its ring closure. -192: [12:01:00] SLN Parser error: Ring closure 1 does not have a corresponding opener. -192: [12:01:00] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -192: [12:01:00] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -192: [12:01:00] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -192: [12:01:00] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -192: [12:01:00] SLN Parse Error: syntax error while parsing: CH4 fff -192: [12:01:00] Failed parsing SLN 'CH4 fff' -192: [12:01:00] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -192: [12:01:00] Failed parsing SLN 'C[charge=+1] foo' -192: [12:01:00] Query property 'is' ignored on non-query atom -192: [12:01:00] Query property 'is' ignored on non-query atom -151/235 Test #192: testSLNParse ........................... Passed 0.08 sec +192: [09:21:21] SLN Parse Error: syntax error while parsing: CH4[I=13] +192: [09:21:21] Failed parsing SLN 'CH4[I=13]' +192: [09:21:21] SLN Parser error: Atom ID 1 appears *after* its ring closure. +192: [09:21:21] SLN Parser error: Ring closure 1 does not have a corresponding opener. +192: [09:21:21] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +192: [09:21:21] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +192: [09:21:21] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +192: [09:21:21] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +192: [09:21:21] SLN Parse Error: syntax error while parsing: CH4 fff +192: [09:21:21] Failed parsing SLN 'CH4 fff' +192: [09:21:21] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +192: [09:21:21] Failed parsing SLN 'C[charge=+1] foo' +192: [09:21:21] Query property 'is' ignored on non-query atom +192: [09:21:21] Query property 'is' ignored on non-query atom +173/235 Test #192: testSLNParse ........................... Passed 0.10 sec test 193 Start 193: pySLNParse 193: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/Wrap/testSLN.py" 193: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap 193: Test timeout computed to be: 1500 -122: =>start test GETAWAY -122: [12:01:00] test on : 365 molecules done -152/235 Test #122: testGETAWAY ............................ Passed 5.02 sec +174/235 Test #191: pyMolInterchange ....................... Passed 1.40 sec test 194 Start 194: pyGraphMolWrap 194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rough_test.py" 194: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 194: Test timeout computed to be: 1500 -147: [12:01:00] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -183: Randomness seeded to: 3156303335 -183: =============================================================================== -183: All tests passed (171 assertions in 5 test cases) -183: -153/235 Test #183: substructLibraryCatchTest .............. Passed 2.21 sec +29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +29: All 191 tests passed +193: .. +193: ---------------------------------------------------------------------- +193: Ran 2 tests in 0.012s +193: +193: OK +175/235 Test #193: pySLNParse ............................. Passed 0.86 sec test 195 Start 195: pyTestConformerWrap @@ -30012,228 +31133,70 @@ 195: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 195: Test timeout computed to be: 1500 29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -185: [12:01:00] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -147: [12:01:00] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -185: [12:01:00] WARNING: not removing hydrogen atom with dummy atom neighbors -125: Warning: Atom Count for residue GLU150A does not match expected count -182: [12:01:01] done -182: [12:01:01] ------------------------------------- -182: [12:01:01] Test2 -70: [12:01:01] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -70: [12:01:01] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -187: Randomness seeded to: 316539484 -187: =============================================================================== -187: All tests passed (1475 assertions in 14 test cases) -187: -154/235 Test #187: rgroupCatchTests ....................... Passed 0.48 sec +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... +195: ...... +195: ---------------------------------------------------------------------- +195: Ran 6 tests in 0.030s +195: +195: OK +176/235 Test #195: pyTestConformerWrap .................... Passed 0.77 sec test 196 Start 196: pyTestTrajectory 196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testTrajectory.py" 196: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 196: Test timeout computed to be: 1500 -147: [12:01:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -117: =>start test 2 WHIM custom -117: [12:01:01] test on : 365 molecules done -147: [12:01:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -147: [12:01:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -125: Warning: Atom Count for residue ASN157A does not match expected count -141: [12:01:01] done -141: [12:01:01] ------------------------------------- -141: [12:01:01] Test MMFF multithreading2 -160: file testHandDrawn-5a.svg gave hash 3327818543U not the expected 1567781555U -160: [12:01:01] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -126: Warning: Atom Count for residue GLU150A does not match expected count -160: [12:01:01] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -70: ---------------------------------- -70: ---------------------------------- -70: [12:01:01] -70: -70: **** -70: Pre-condition Violation -70: rlabel out of range for MDL files -70: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp -70: Failed Expression: rlabel >= 0 && rlabel < 100 -70: ---------- -70: Stacktrace: -70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -70: 3# 0x00005589324720FF in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 4# 0x00005589324CB56A in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 5# 0x000055893244B9E3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 6# 0x00007F77AAC33D68 in /lib/x86_64-linux-gnu/libc.so.6 -70: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -70: 8# 0x000055893244BB11 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: ---------- -70: **** -70: -70: [12:01:01] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -160: file testHandDrawn-5b.svg gave hash 2125846125U not the expected 66354106U -160: [12:01:01] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [12:01:01] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -126: Warning: Atom Count for residue ASN157A does not match expected count -191: .. -191: ---------------------------------------------------------------------- -191: Ran 2 tests in 0.046s -191: -191: OK -148: [12:01:01] Molecule does not have explicit Hs. Consider calling AddHs() -193: .. -193: ---------------------------------------------------------------------- -193: Ran 2 tests in 0.023s -193: -193: OK -160: file testHandDrawn-5.png gave hash 2537746017U not the expected 828378555U -160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U -155/235 Test #191: pyMolInterchange ....................... Passed 0.92 sec +188: .................... +188: ---------------------------------------------------------------------- +188: Ran 20 tests in 4.689s +188: +188: OK +177/235 Test #188: pyRGroupDecomposition .................. Passed 5.44 sec test 197 Start 197: pyTestSGroups 197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testSGroups.py" 197: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 197: Test timeout computed to be: 1500 -146: [12:00:56] --------------------------------- -146: [12:00:56] test3 -146: -146: [12:00:56] --------------------------------- -146: [12:00:56] test4 -146: -146: [12:00:56] --------------------------------- -146: [12:00:56] test5 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] test6 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] test15Dists -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] test Issue 215 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] testMultipleConfs -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] testMultipleConfsExpTors -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] testIssue227 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] testIssue236 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] testOrdering -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] testIssue244 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] testIssue251 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] testIssue276 -146: [12:01:01] --------------------------------- -146: [12:01:01] testIssue284 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] testIssue285 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] testIssue355 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] testRandomCoords -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] test sf.net issue 1989539 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] test sf.net issue 2091864 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] test constrained embedding -146: -146: [12:01:01] ssd: 0.0752641 -156/235 Test #193: pySLNParse ............................. Passed 0.80 sec -test 198 - Start 198: pyTestThreads - -198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testThreads.py" -198: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -198: Test timeout computed to be: 1500 -146: [12:01:01] ssd: 0.0659363 -141: [12:01:01] done -141: [12:01:01] ------------------------------------- -141: [12:01:01] Test MMFF multithreading3 -182: [12:01:01] done -151: 4521910497 -182: [12:01:01] ------------------------------------- -182: [12:01:01] Test3 (stereo options) -195: ...... -195: ---------------------------------------------------------------------- -195: Ran 6 tests in 0.050s -195: -195: OK -160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test Issue252: Bad definitions for Crippen atom types. -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test calculation of ChiVs. -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test calculation of ChiNs. -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test calculation of HallKierAlpha. -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test calculation of Kappa1. -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test calculation of Kappa2. -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test calculation of Kappa3. -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test Crippen atom type calculations. -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test ring descriptors -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test other count descriptors. -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test MQN -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test GitHub Issue 56. -111: [12:01:01] WARNING: not removing hydrogen atom without neighbors -111: [12:01:01] WARNING: not removing hydrogen atom without neighbors -111: [12:01:01] WARNING: not removing hydrogen atom without neighbors -111: [12:01:01] WARNING: not removing hydrogen atom without neighbors -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test Github92: Bad Crippen atom type for pyrrole H. -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test Github362: order dependence in Kier-Hall descriptors. -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test calculation of spiro and bridgehead counts. -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test Github694: ExactMolWt ignoring the mass of the electron -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Testing Properties and KitchenSink -196: [12:01:01] +194: ..............[09:21:24] SMARTS Parse Error: syntax error while parsing: fiib +194: [09:21:24] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +194: ....[09:21:24] ERROR: Problems encountered parsing data fields +194: [09:21:24] ERROR: moving to the beginning of the next molecule +194: [09:21:24] ERROR: Problems encountered parsing data fields +194: [09:21:24] ERROR: moving to the beginning of the next molecule +194: [09:21:24] Spurious data before the first property will be ignored +194: [09:21:24] Property will be truncated after the first blank line +194: [09:21:24] Property will be truncated after the first blank line +194: [09:21:24] Property will be truncated after the first blank line +194: [09:21:24] ERROR: Problems encountered parsing data fields +194: [09:21:24] ERROR: moving to the beginning of the next molecule +194: [09:21:24] ERROR: Problems encountered parsing data fields +194: [09:21:24] ERROR: moving to the beginning of the next molecule +194: [09:21:24] Spurious data before the first property will be ignored +194: [09:21:24] Property will be truncated after the first blank line +194: [09:21:24] Property will be truncated after the first blank line +194: [09:21:24] Property will be truncated after the first blank line +194: [09:21:24] ERROR: Problems encountered parsing data fields +194: [09:21:24] ERROR: moving to the beginning of the next molecule +194: [09:21:24] Property will be truncated after the first blank line +194: [09:21:24] ERROR: Problems encountered parsing data fields +194: [09:21:24] ERROR: moving to the beginning of the next molecule +194: [09:21:24] Property will be truncated after the first blank line +194: .[09:21:24] SMILES Parse Error: syntax error while parsing: fail +194: [09:21:24] SMILES Parse Error: check for mistakes around position 1: +194: [09:21:24] fail +194: [09:21:24] ^ +194: [09:21:24] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +194: [09:21:24] ERROR: Smiles parse error on line 2 +194: [09:21:24] ERROR: Cannot create molecule from : 'fail' +194: >>> This may result in an infinite loop. It should finish almost instantly +194: <<< OK, it finished. +194: ............[09:21:24] Explicit valence for atom # 1 C, 5, is greater than permitted +194: ......[09:21:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +194: [09:21:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +194: [09:21:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +194: [09:21:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +196: [09:21:24] 196: 196: **** 196: Pre-condition Violation @@ -30247,23 +31210,23 @@ 196: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x00007F1060B4066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x00007F4535D1066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x00007F105E7B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x00007F105E7B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x00007F105E7B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x00007F105E7B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x00007F105E7B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x00007F45337B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x00007F45337B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x00007F45337B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x00007F45337B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x00007F45337B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x00007F1060B3D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x00007F4535D0D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005BEE79 in /usr/bin/python3 @@ -30295,13 +31258,14 @@ 196: 50# 0x000000000067EB1E in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x00007F10612E8D68 in /lib/x86_64-linux-gnu/libc.so.6 +196: 53# 0x00007F45364C6D68 in /lib/x86_64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: .[12:01:01] +194: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| +196: .[09:21:24] 196: 196: **** 196: Pre-condition Violation @@ -30315,23 +31279,23 @@ 196: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x00007F1060B4066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x00007F4535D1066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x00007F105E7B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x00007F105E7B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x00007F105E7B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x00007F105E7B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x00007F105E7B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x00007F45337B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x00007F45337B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x00007F45337B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x00007F45337B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x00007F45337B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x00007F1060B3D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x00007F4535D0D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005BEE79 in /usr/bin/python3 @@ -30363,234 +31327,691 @@ 196: 50# 0x000000000067EB1E in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x00007F10612E8D68 in /lib/x86_64-linux-gnu/libc.so.6 +196: 53# 0x00007F45364C6D68 in /lib/x86_64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- -111: [12:01:01] ---Caught keyerror (bad property name)--- -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test USR Descriptor 196: **** 196: -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test Github #1973: support P and S terms for TPSA calculation -111: [12:01:01] done -111: [12:01:01] ------------------------------------- -111: [12:01:01] Test Github #2948: Empty molecule has non-zero LabuteASA -111: [12:01:01] done -157/235 Test #111: testDescriptors ........................ Passed 6.55 sec -test 199 - Start 199: pyTestMultithreadedMolSupplier - -199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" -199: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -199: Test timeout computed to be: 1500 -158/235 Test #195: pyTestConformerWrap .................... Passed 1.07 sec -test 200 - Start 200: pyTestPropertyLists - -200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testPropertyLists.py" -200: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -200: Test timeout computed to be: 1500 -117: =>start test 1 WHIM custom -117: [12:01:02] test on : 365 molecules done -182: [12:01:02] Done (stereo options) -182: [12:01:02] ------------------------------------- -182: [12:01:02] Test4 (trusted smiles) -143: [12:01:02] done -143: [12:01:02] ------------------------------------- -143: [12:01:02] Test UFF multithreading2 -148: [12:01:02] Molecule does not have explicit Hs. Consider calling AddHs() -146: [12:01:01] --------------------------------- -146: [12:01:01] test sf.net issue 2091974 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] test sf.net issue 2835784 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] test sf.net issue 3019283 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] test sf.net issue 3238580 -146: -146: [12:01:01] --------------------------------- -146: [12:01:01] test sf.net issue 3483968 -146: -146: [12:01:02] --------------------------------- -146: [12:01:02] test github issue 55 -146: -146: [12:01:02] --------------------------------- -146: [12:01:02] test1 -146: -146: [12:01:02] --------------------------------- -146: [12:01:02] test multi-threading -146: -146: building molecules -141: [12:01:02] done -141: [12:01:02] ------------------------------------- -141: [12:01:02] Testing github 162: Incorrect SMILES after MMFF parameterization . -141: [12:01:02] done -141: [12:01:02] ------------------------------------- -141: [12:01:02] Testing github 224: crash during MMFF parameterization . -141: [12:01:02] done -141: [12:01:02] ------------------------------------- -141: [12:01:02] Testing github6728: crash due to missing stretch-bend params. -159/235 Test #141: testMMFFForceFieldHelpers .............. Passed 5.77 sec -test 201 - Start 201: pyCDXMLTest - -201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/test_cdxml.py" -201: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -201: Test timeout computed to be: 1500 -146: generating reference data -70: [12:01:02] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -70: [12:01:02] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -160: [12:01:02] unrecognized bond typefile testGithub4238_1.png gave hash 1999044295U not the expected 2623427676U -160: file testGithub4323_1.png gave hash 1674734291U not the expected 3075787867U -182: [12:01:02] Done (trusted smiles) -182: [12:01:02] ------------------------------------- -182: [12:01:02] Testing C++ docs -182: [12:01:02] Done (C++ doc tests) -182: [12:01:02] ------------------------------------- -182: [12:01:02] Testing C++ ring query: PatternHolder -182: [12:01:02] Done (C++ ring query tests) -182: [12:01:02] ------------------------------------- -182: [12:01:02] Testing C++ ring query: TautomerPatternHolder -182: [12:01:02] Done (C++ ring query tests) -182: [12:01:02] ------------------------------------- -182: [12:01:02] Add Patterns +194: ........[09:21:24] non-ring atom 0 marked aromatic +194: [09:21:24] non-ring atom 0 marked aromatic +194: [09:21:24] +194: +194: **** +194: Range Error +194: idx +194: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +194: Failed Expression: 12 < 6 +194: ---------- +194: Stacktrace: +194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +194: 4# 0x00007F6BB8681CE0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 6# 0x00007F6BBAF2066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so +194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +194: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x00007F6BB85B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x00007F6BB85B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x00007F6BB85B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x00007F6BB85B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 21# 0x00007F6BB85B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +194: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +194: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 27# 0x00007F6BBAF1D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 28# _PyObject_MakeTpCall in /usr/bin/python3 +194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 30# 0x00000000005BEE79 in /usr/bin/python3 +194: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 32# 0x0000000000547080 in /usr/bin/python3 +194: 33# 0x00000000006AB720 in /usr/bin/python3 +194: 34# _PyObject_MakeTpCall in /usr/bin/python3 +194: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 36# 0x00000000005BEE79 in /usr/bin/python3 +194: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 38# 0x0000000000547080 in /usr/bin/python3 +194: 39# 0x00000000006AB720 in /usr/bin/python3 +194: 40# _PyObject_MakeTpCall in /usr/bin/python3 +194: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 42# 0x00000000005BEE79 in /usr/bin/python3 +194: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 44# 0x0000000000547080 in /usr/bin/python3 +194: 45# 0x00000000006AB720 in /usr/bin/python3 +194: 46# _PyObject_MakeTpCall in /usr/bin/python3 +194: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 48# 0x000000000059582E in /usr/bin/python3 +194: 49# _PyObject_MakeTpCall in /usr/bin/python3 +194: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 51# PyEval_EvalCode in /usr/bin/python3 +194: 52# 0x000000000066A861 in /usr/bin/python3 +194: 53# 0x000000000066670C in /usr/bin/python3 +194: 54# 0x000000000067F713 in /usr/bin/python3 +194: 55# 0x000000000067ECE3 in /usr/bin/python3 +194: 56# 0x000000000067EB1E in /usr/bin/python3 +194: 57# Py_RunMain in /usr/bin/python3 +194: 58# Py_BytesMain in /usr/bin/python3 +194: 59# 0x00007F6BBB73ED68 in /lib/x86_64-linux-gnu/libc.so.6 +194: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +194: 61# _start in /usr/bin/python3 +194: ---------- +194: **** +194: +194: [09:21:24] non-ring atom 0 marked aromatic +194: [09:21:24] non-ring atom 0 marked aromatic +194: [09:21:24] +194: +194: **** +194: Range Error +194: idx +194: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +194: Failed Expression: 12 < 6 +194: ---------- +194: Stacktrace: +194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +194: 4# 0x00007F6BB8681CE0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 6# 0x00007F6BBAF2066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so +194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +194: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x00007F6BB85B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x00007F6BB85B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x00007F6BB85B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x00007F6BB85B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 21# 0x00007F6BB85B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +194: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +194: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 27# 0x00007F6BBAF1D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 28# _PyObject_MakeTpCall in /usr/bin/python3 +194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 30# 0x00000000005BEE79 in /usr/bin/python3 +194: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 32# 0x0000000000547080 in /usr/bin/python3 +194: 33# 0x00000000006AB720 in /usr/bin/python3 +194: 34# _PyObject_MakeTpCall in /usr/bin/python3 +194: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 36# 0x00000000005BEE79 in /usr/bin/python3 +194: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 38# 0x0000000000547080 in /usr/bin/python3 +194: 39# 0x00000000006AB720 in /usr/bin/python3 +194: 40# _PyObject_MakeTpCall in /usr/bin/python3 +194: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 42# 0x00000000005BEE79 in /usr/bin/python3 +194: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 44# 0x0000000000547080 in /usr/bin/python3 +194: 45# 0x00000000006AB720 in /usr/bin/python3 +194: 46# _PyObject_MakeTpCall in /usr/bin/python3 +194: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 48# 0x000000000059582E in /usr/bin/python3 +194: 49# _PyObject_MakeTpCall in /usr/bin/python3 +194: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 51# PyEval_EvalCode in /usr/bin/python3 +194: 52# 0x000000000066A861 in /usr/bin/python3 +194: 53# 0x000000000066670C in /usr/bin/python3 +194: 54# 0x000000000067F713 in /usr/bin/python3 +194: 55# 0x000000000067ECE3 in /usr/bin/python3 +194: 56# 0x000000000067EB1E in /usr/bin/python3 +194: 57# Py_RunMain in /usr/bin/python3 +194: 58# Py_BytesMain in /usr/bin/python3 +194: 59# 0x00007F6BBB73ED68 in /lib/x86_64-linux-gnu/libc.so.6 +194: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +194: 61# _start in /usr/bin/python3 +194: ---------- +194: **** +194: +182: [09:21:24] ------------------------------------- +182: [09:21:24] testing PatternHolder +194: ...............[09:21:24] 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. +194: [09:21:24] 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. +194: ..............[09:21:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +194: [09:21:24] Explicit valence for atom # 1 C, 5, is greater than permitted 197: ............. 197: ---------------------------------------------------------------------- 197: Ran 13 tests in 0.092s 197: 197: OK 197: Testing SubstanceGroups wrapper -70: [12:01:02] Empty atom list: 'M ALS 1 0 F' on line 8. -160/235 Test #70: fileParsersTest1 ....................... Passed 7.39 sec -test 202 - Start 202: molStandardizeTest - -202: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest -202: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -202: Test timeout computed to be: 1500 -163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -163: Time elapsed 0.000 seconds -163: -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 0.184 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 0.031 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 0.047 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 0.316 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 0.245 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 0.292 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 0.344 seconds -163: -163: testSegFault() -163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.035 seconds -163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.047 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 0.063 seconds -163: -163: testThreshold() -163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -163: Time elapsed 0.000 seconds -163: -163: testRing1() -163: MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds -163: Time elapsed 1.581 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 1.135 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 0.499 seconds -163: -163: testAtomCompareIsotopes() -163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds -163: Time elapsed 0.000 seconds -163: -163: testAtomCompareAnyAtom() -163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -163: Time elapsed 0.000 seconds -163: -163: testAtomCompareAnyAtom() -163: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -163: Time elapsed 0.000 seconds -163: -163: testAtomCompareAnyAtom() -163: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds -163: Time elapsed 0.000 seconds -163: -163: testAtomCompareAnyAtom() -163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds -163: Time elapsed 0.000 seconds -163: -163: testJnk1LigandsDistance() -163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds -163: Time elapsed 0.023 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 -194: ..............[12:01:02] SMARTS Parse Error: syntax error while parsing: fiib -194: [12:01:02] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -161/235 Test #197: pyTestSGroups .......................... Passed 0.93 sec -test 203 - Start 203: molNormalizeTest +178/235 Test #197: pyTestSGroups .......................... Passed 1.65 sec +test 198 + Start 198: pyTestThreads -203: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest -203: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -203: Test timeout computed to be: 1500 -194: ....[12:01:02] ERROR: Problems encountered parsing data fields -194: [12:01:02] ERROR: moving to the beginning of the next molecule -194: [12:01:02] ERROR: Problems encountered parsing data fields -194: [12:01:02] ERROR: moving to the beginning of the next molecule -194: [12:01:02] Spurious data before the first property will be ignored -194: [12:01:02] Property will be truncated after the first blank line -194: [12:01:02] Property will be truncated after the first blank line -194: [12:01:02] Property will be truncated after the first blank line -194: [12:01:02] ERROR: Problems encountered parsing data fields -194: [12:01:02] ERROR: moving to the beginning of the next molecule -194: [12:01:02] ERROR: Problems encountered parsing data fields -194: [12:01:02] ERROR: moving to the beginning of the next molecule -194: [12:01:02] Spurious data before the first property will be ignored -194: [12:01:02] Property will be truncated after the first blank line -194: [12:01:02] Property will be truncated after the first blank line -194: [12:01:02] Property will be truncated after the first blank line -194: [12:01:02] ERROR: Problems encountered parsing data fields -194: [12:01:02] ERROR: moving to the beginning of the next molecule -194: [12:01:02] Property will be truncated after the first blank line -194: [12:01:02] ERROR: Problems encountered parsing data fields -194: [12:01:02] ERROR: moving to the beginning of the next molecule -194: [12:01:02] Property will be truncated after the first blank line -194: .[12:01:02] SMILES Parse Error: syntax error while parsing: fail -194: [12:01:02] SMILES Parse Error: check for mistakes around position 1: -194: [12:01:02] fail -194: [12:01:02] ^ -194: [12:01:02] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -194: [12:01:02] ERROR: Smiles parse error on line 2 -194: [12:01:02] ERROR: Cannot create molecule from : 'fail' -194: >>> This may result in an infinite loop. It should finish almost instantly -194: <<< OK, it finished. -196: .[12:01:02] +198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testThreads.py" +198: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +198: Test timeout computed to be: 1500 +182: [09:21:25] ------------------------------------- +182: [09:21:25] testing TautomerPatternHolder +185: bulk +182: [09:21:26] ------------------------------------- +182: [09:21:26] testSegFaultInHolder +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^[09:21:26] [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] +182: SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1:[09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'1[09:21:26] SMILES: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: syntax error[09:21:26] [09:21:26] Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfSMILES Parse Error: syntax error while parsing: dsafsdf[09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf[09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1:[09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: +182: SMILES[09:21:26] Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: ' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: syntax error[09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +196: .[09:21:26] 196: 196: **** +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 196: Range Error 196: snapshotNum 196: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30603,23 +32024,23 @@ 196: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 6# 0x00007F1060B4066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 6# 0x00007F4535D1066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x00007F105E7B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x00007F105E7B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x00007F105E7B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x00007F105E7B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 16# 0x00007F105E7B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x00007F45337B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x00007F45337B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x00007F45337B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x00007F45337B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 16# 0x00007F45337B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 22# 0x00007F1060B3D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 22# 0x00007F4535D0D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 23# _PyObject_MakeTpCall in /usr/bin/python3 196: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 25# 0x00000000005BEE79 in /usr/bin/python3 @@ -30651,18 +32072,265 @@ 196: 51# 0x000000000067EB1E in /usr/bin/python3 196: 52# Py_RunMain in /usr/bin/python3 196: 53# Py_BytesMain in /usr/bin/python3 -196: 54# 0x00007F10612E8D68 in /lib/x86_64-linux-gnu/libc.so.6 +196: 54# 0x00007F45364C6D68 in /lib/x86_64-linux-gnu/libc.so.6 196: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 196: 56# _start in /usr/bin/python3 196: ---------- -143: [12:01:02] done -143: [12:01:02] ------------------------------------- -143: [12:01:02] Test UFF multithreading3 196: **** 196: -196: .[12:01:02] +196: .[09:21:26] 196: 196: **** +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 196: Pre-condition Violation 196: The trajectory must have dimension == 3 196: Violation occurred on line 113 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30674,23 +32342,23 @@ 196: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x00007F1060B4066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x00007F4535D1066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x00007F105E7B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x00007F105E7B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x00007F105E7B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x00007F105E7B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x00007F105E7B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x00007F45337B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x00007F45337B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x00007F45337B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x00007F45337B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x00007F45337B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x00007F1060B3D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x00007F4535D0D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005BEE79 in /usr/bin/python3 @@ -30722,21 +32390,265 @@ 196: 50# 0x000000000067EB1E in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x00007F10612E8D68 in /lib/x86_64-linux-gnu/libc.so.6 +196: 53# 0x00007F45364C6D68 in /lib/x86_64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: ..[12:01:02] +196: ..[09:21:26] 196: 196: **** -199: .s. -199: ---------------------------------------------------------------------- -199: Ran 3 tests in 0.269s -199: -199: OK (skipped=1) -199: Testing Smiles and SD MultithreadedMolSupplier +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [09:21:26] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [09:21:26] SMILES Parse Error: check for mistakes around position 1: +182: [09:21:26] dsafsdf +182: [09:21:26] ^ +182: [09:21:26] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 196: Pre-condition Violation 196: The trajectory must have dimension == 3 196: Violation occurred on line 154 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30748,23 +32660,23 @@ 196: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x00007F1060B4066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x00007F4535D1066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x00007F105E7B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x00007F105E7B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x00007F105E7B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x00007F105E7B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x00007F105E7B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x00007F45337B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x00007F45337B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x00007F45337B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x00007F45337B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x00007F45337B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x00007F1060B3D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x00007F4535D0D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005BEE79 in /usr/bin/python3 @@ -30796,15 +32708,16 @@ 196: 50# 0x000000000067EB1E in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x00007F10612E8D68 in /lib/x86_64-linux-gnu/libc.so.6 +196: 53# 0x00007F45364C6D68 in /lib/x86_64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: .[12:01:02] +196: .[09:21:26] 196: 196: **** +194: ............................[09:21:26] unable to set wavy bonds for double bonds: 3 196: Pre-condition Violation 196: d_pos must not be NULL 196: Violation occurred on line 23 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30816,23 +32729,23 @@ 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x00007F1060B4066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x00007F4535D1066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x00007F105E7B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x00007F105E7B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x00007F105E7B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x00007F105E7B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x00007F105E7B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x00007F45337B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x00007F45337B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x00007F45337B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x00007F45337B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x00007F45337B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x00007F1060B3D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x00007F4535D0D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005BEE79 in /usr/bin/python3 @@ -30864,15 +32777,17 @@ 196: 50# 0x000000000067EB1E in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x00007F10612E8D68 in /lib/x86_64-linux-gnu/libc.so.6 +196: 53# 0x00007F45364C6D68 in /lib/x86_64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: [12:01:02] +196: [09:21:26] 196: 196: **** +182: [09:21:26] ------------------------------------- +182: [09:21:26] Results do not depend on numThreads 196: Pre-condition Violation 196: d_trajectory must not be NULL 196: Violation occurred on line 24 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30884,23 +32799,23 @@ 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x00007F1060B4066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x00007F4535D1066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x00007F105E7B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x00007F105E7B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x00007F105E7B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x00007F105E7B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x00007F105E7B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x00007F45337B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x00007F45337B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x00007F45337B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x00007F45337B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x00007F45337B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x00007F1060B3D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x00007F4535D0D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005BEE79 in /usr/bin/python3 @@ -30932,13 +32847,13 @@ 196: 50# 0x000000000067EB1E in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x00007F10612E8D68 in /lib/x86_64-linux-gnu/libc.so.6 +196: 53# 0x00007F45364C6D68 in /lib/x86_64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: .[12:01:02] +196: .[09:21:26] 196: 196: **** 196: Range Error @@ -30953,23 +32868,23 @@ 196: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 6# 0x00007F1060B4066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 6# 0x00007F4535D1066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x00007F105E7B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x00007F105E7B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x00007F105E7B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x00007F105E7B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 16# 0x00007F105E7B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x00007F45337B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x00007F45337B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x00007F45337B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x00007F45337B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 16# 0x00007F45337B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 22# 0x00007F1060B3D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 22# 0x00007F4535D0D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 23# _PyObject_MakeTpCall in /usr/bin/python3 196: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 25# 0x00000000005BEE79 in /usr/bin/python3 @@ -31001,13 +32916,13 @@ 196: 51# 0x000000000067EB1E in /usr/bin/python3 196: 52# Py_RunMain in /usr/bin/python3 196: 53# Py_BytesMain in /usr/bin/python3 -196: 54# 0x00007F10612E8D68 in /lib/x86_64-linux-gnu/libc.so.6 +196: 54# 0x00007F45364C6D68 in /lib/x86_64-linux-gnu/libc.so.6 196: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 196: 56# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: [12:01:02] +196: [09:21:26] 196: 196: **** 196: Range Error @@ -31021,23 +32936,23 @@ 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x00007F1060B4066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x00007F4535D1066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x00007F105E7B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x00007F105E7B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x00007F105E7B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x00007F105E7B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x00007F105E7B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x00007F45337B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x00007F45337B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x00007F45337B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x00007F45337B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x00007F45337B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x00007F1060B3D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x00007F4535D0D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005BEE79 in /usr/bin/python3 @@ -31069,13 +32984,13 @@ 196: 50# 0x000000000067EB1E in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x00007F10612E8D68 in /lib/x86_64-linux-gnu/libc.so.6 +196: 53# 0x00007F45364C6D68 in /lib/x86_64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: .[12:01:02] +196: .[09:21:26] 196: 196: **** 196: Range Error @@ -31090,23 +33005,23 @@ 196: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 6# 0x00007F1060B4066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 6# 0x00007F4535D1066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x00007F105E7B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x00007F105E7B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x00007F105E7B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x00007F105E7B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 16# 0x00007F105E7B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x00007F45337B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x00007F45337B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x00007F45337B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x00007F45337B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 16# 0x00007F45337B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 22# 0x00007F1060B3D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 22# 0x00007F4535D0D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 23# _PyObject_MakeTpCall in /usr/bin/python3 196: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 25# 0x00000000005BEE79 in /usr/bin/python3 @@ -31138,13 +33053,13 @@ 196: 51# 0x000000000067EB1E in /usr/bin/python3 196: 52# Py_RunMain in /usr/bin/python3 196: 53# Py_BytesMain in /usr/bin/python3 -196: 54# 0x00007F10612E8D68 in /lib/x86_64-linux-gnu/libc.so.6 +196: 54# 0x00007F45364C6D68 in /lib/x86_64-linux-gnu/libc.so.6 196: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 196: 56# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: [12:01:02] +196: [09:21:26] 196: 196: **** 196: Pre-condition Violation @@ -31158,23 +33073,23 @@ 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x00007F1060B4066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x00007F4535D1066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x00007F105E7B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x00007F105E7B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x00007F105E7B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x00007F105E7B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x00007F105E7B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x00007F45337B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x00007F45337B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x00007F45337B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x00007F45337B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x00007F45337B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x00007F1060B3D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x00007F4535D0D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005BEE79 in /usr/bin/python3 @@ -31206,15 +33121,89 @@ 196: 50# 0x000000000067EB1E in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x00007F10612E8D68 in /lib/x86_64-linux-gnu/libc.so.6 +196: 53# 0x00007F45364C6D68 in /lib/x86_64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: [12:01:02] +196: [09:21:26] 196: 196: **** +194: .............[09:21:26] +194: +194: **** +194: Range Error +194: idx +194: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +194: Failed Expression: 6 < 5 +194: ---------- +194: Stacktrace: +194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +194: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 6# 0x00007F6BBAF2066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so +194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +194: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x00007F6BB85B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x00007F6BB85B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x00007F6BB85B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x00007F6BB85B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 21# 0x00007F6BB85B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +194: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +194: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 27# 0x00007F6BBAF1D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 28# _PyObject_MakeTpCall in /usr/bin/python3 +194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 30# 0x00000000005BEE79 in /usr/bin/python3 +194: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 32# 0x0000000000547080 in /usr/bin/python3 +194: 33# 0x00000000006AB720 in /usr/bin/python3 +194: 34# _PyObject_MakeTpCall in /usr/bin/python3 +194: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 36# 0x00000000005BEE79 in /usr/bin/python3 +194: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 38# 0x0000000000547080 in /usr/bin/python3 +194: 39# 0x00000000006AB720 in /usr/bin/python3 +194: 40# _PyObject_MakeTpCall in /usr/bin/python3 +194: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 42# 0x00000000005BEE79 in /usr/bin/python3 +194: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 44# 0x0000000000547080 in /usr/bin/python3 +194: 45# 0x00000000006AB720 in /usr/bin/python3 +194: 46# _PyObject_MakeTpCall in /usr/bin/python3 +194: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 48# 0x000000000059582E in /usr/bin/python3 +194: 49# _PyObject_MakeTpCall in /usr/bin/python3 +194: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +194: 51# PyEval_EvalCode in /usr/bin/python3 +194: 52# 0x000000000066A861 in /usr/bin/python3 +194: 53# 0x000000000066670C in /usr/bin/python3 +194: 54# 0x000000000067F713 in /usr/bin/python3 +194: 55# 0x000000000067ECE3 in /usr/bin/python3 +194: 56# 0x000000000067EB1E in /usr/bin/python3 +194: 57# Py_RunMain in /usr/bin/python3 +194: 58# Py_BytesMain in /usr/bin/python3 +194: 59# 0x00007F6BBB73ED68 in /lib/x86_64-linux-gnu/libc.so.6 +194: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +194: 61# _start in /usr/bin/python3 +194: ---------- +194: **** +194: 196: Pre-condition Violation 196: d_dimension must be == 2 196: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -31226,23 +33215,23 @@ 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x00007F1060B4066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x00007F4535D1066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x00007F105E7B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x00007F105E7B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x00007F105E7B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x00007F105E7B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x00007F105E7B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x00007F45337B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x00007F45337B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x00007F45337B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x00007F45337B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x00007F45337B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x00007F1060B3D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x00007F4535D0D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005BEE79 in /usr/bin/python3 @@ -31274,7 +33263,7 @@ 196: 50# 0x000000000067EB1E in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x00007F10612E8D68 in /lib/x86_64-linux-gnu/libc.so.6 +196: 53# 0x00007F45364C6D68 in /lib/x86_64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- @@ -31282,190 +33271,92 @@ 196: 196: . 196: ---------------------------------------------------------------------- -196: Ran 9 tests in 0.817s +196: Ran 9 tests in 2.027s 196: 196: OK 196: Testing Trajectory wrapper -203: [12:01:02] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -194: ............[12:01:02] Explicit valence for atom # 1 C, 5, is greater than permitted -162/235 Test #199: pyTestMultithreadedMolSupplier ......... Passed 0.77 sec -test 204 - Start 204: molValidateTest +179/235 Test #196: pyTestTrajectory ....................... Passed 3.45 sec +test 199 + Start 199: pyTestMultithreadedMolSupplier -204: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest -204: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -204: Test timeout computed to be: 1500 -148: [12:01:02] Molecule does not have explicit Hs. Consider calling AddHs() -172: .... -172: ---------------------------------------------------------------------- -172: Ran 14 tests in 4.305s -172: -172: OK -163/235 Test #196: pyTestTrajectory ....................... Passed 1.69 sec -test 205 - Start 205: molChargeTest +199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" +199: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +199: Test timeout computed to be: 1500 +199: .s. +199: ---------------------------------------------------------------------- +199: Ran 3 tests in 0.450s +199: +199: OK (skipped=1) +199: Testing Smiles and SD MultithreadedMolSupplier +180/235 Test #199: pyTestMultithreadedMolSupplier ......... Passed 1.74 sec +test 200 + Start 200: pyTestPropertyLists -205: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest -205: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -205: Test timeout computed to be: 1500 -194: ......[12:01:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -194: [12:01:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -194: [12:01:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -194: [12:01:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -194: .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)| -200: [12:01:02] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -200: [12:01:02] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -200: [12:01:02] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -200: .[12:01:02] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -200: [12:01:02] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -200: [12:01:02] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -163: Time elapsed 0.002 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 0.014 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 0.266 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 0.074 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 0.0017 seconds. bond[0]=6 -163: STATISTICS: -163: Total Growing Steps = 1, MCS found on 1 step, for 0.0017 seconds -163: Initial Seeds = 1, Mismatched 0 -163: Inspected Seeds = 2 -163: Rejected by BestSize = 0 -163: IndividualBondExcluded = 0 -163: MatchCheck Seeds = 2 -163: MatchCalls = 2 -163: MatchFound = 1 -163: fastMatchCalls = 1 -163: fastMatchFound = 0 -163: slowMatchCalls = 2 -163: slowMatchFound = 1 -163: DupCacheFound = 0 0 matched, 0 mismatched -163: HashCache size = 1 keys -163: HashCache size = 1 entries -163: FindHashInCache = 2 -163: HashFoundInCache= 0 -163: ExactMatchCalls = 0 -163: ExactMatchFound = 0 -163: Time elapsed 0.002 seconds -163: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 -163: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 -163: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 -163: res sub = 1 size=3 -163: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -163: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 -163: res sub = 1 size=3 -163: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -163: test target = CC[C@H](F)Cl query = CCC useChirality = 0 -163: res sub = 1 size=3 -163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -163: test target = CC[C@H](F)Cl query = CCC useChirality = 1 -163: res sub = 1 size=3 -163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -163: test target = CCC(F)Cl query = CC useChirality = 0 -163: res sub = 1 size=2 -163: MCS: [#6]-[#6] 2 atoms, 1 bonds -163: test target = CCC(F)Cl query = CC useChirality = 1 -163: res sub = 1 size=2 -163: MCS: [#6]-[#6] 2 atoms, 1 bonds -163: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 -163: res sub = 1 size=4 -163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 -163: res sub = 1 size=4 -163: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 -163: res sub = 0 size=0 -163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -163: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 -163: res sub = 0 size=0 -163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 -163: res sub = 0 size=0 -163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -163: test target = OC(F)CCl query = OC(F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = OC(F)CCl query = OC(F)C useChirality = 1 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 -200: ...[12:01:02] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -200: [12:01:02] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -200: [12:01:02] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testPropertyLists.py" +200: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +200: Test timeout computed to be: 1500 +200: [09:21:29] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +200: [09:21:29] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +200: [09:21:29] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +200: .[09:21:29] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +200: [09:21:29] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +200: [09:21:29] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +200: ...[09:21:29] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +200: [09:21:29] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +200: [09:21:29] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 200: . 200: ---------------------------------------------------------------------- -200: Ran 5 tests in 0.062s +200: Ran 5 tests in 0.053s 200: 200: OK -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 -163: res sub = 0 size=0 -163: MCS: [#9] 1 atoms, 0 bonds -163: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 -163: res sub = 1 size=4 -163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -163: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 -163: res sub = 0 size=0 -163: MCS: [#9] 1 atoms, 0 bonds -163: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 -163: res sub = 1 size=3 -163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -163: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 -163: res sub = 1 size=3 -163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 -163: res sub = 1 size=3 -163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -163: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 -163: res sub = 1 size=3 -163: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -163: -163: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> -163: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 -163: res sub = 1 size=3 -163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -163: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 -163: res sub = 1 size=3 -163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -163: done -194: ........[12:01:02] non-ring atom 0 marked aromatic -194: [12:01:02] non-ring atom 0 marked aromatic -194: [12:01:02] -194: -194: **** -148: [12:01:02] Molecule does not have explicit Hs. Consider calling AddHs() +181/235 Test #200: pyTestPropertyLists .................... Passed 1.12 sec +test 201 + Start 201: pyCDXMLTest + +201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/test_cdxml.py" +201: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +201: Test timeout computed to be: 1500 +194: ....................[09:21:29] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [09:21:29] Explicit valence for atom # 6 F, 2, is greater than permitted +194: [09:21:29] Can't kekulize mol. Unkekulized atoms: 3 4 5 +194: .................[09:21:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +201: . +201: ---------------------------------------------------------------------- +201: Ran 1 test in 0.022s +201: +201: OK +185: bulk, no symmetry +182/235 Test #201: pyCDXMLTest ............................ Passed 1.17 sec +test 202 + Start 202: molStandardizeTest + +202: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest +202: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +202: Test timeout computed to be: 1500 +185: [09:21:33] Relabelling existing label +185: Best mapping +183/235 Test #185: testRGroupDecomp ....................... Passed 17.97 sec +test 203 + Start 203: molNormalizeTest + +203: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest +203: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +203: Test timeout computed to be: 1500 +203: [09:21:33] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +203: [09:21:33] Initializing Normalizer +203: [09:21:33] Running Normalizer +203: [09:21:33] Rule applied: BrokenazidetoN=N+=N- +203: [09:21:33] Initializing Normalizer +203: [09:21:33] Running Normalizer +203: [09:21:33] Initializing Normalizer +203: [09:21:33] Running Normalizer +184/235 Test #203: molNormalizeTest ....................... Passed 0.23 sec +test 204 + Start 204: molValidateTest + +204: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest +204: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +204: Test timeout computed to be: 1500 204: ERROR: [FeaturesValidation] Query atom 0 is not allowed 204: ERROR: [FeaturesValidation] Dummy atom 0 is not allowed 204: ERROR: [FeaturesValidation] Query bond 0 is not allowed @@ -31477,82 +33368,6 @@ 204: ERROR: [FeaturesValidation] Bond 6 of aromatic type is not allowed 204: ERROR: [FeaturesValidation] Bond 2 of dative type is not allowed 204: ERROR: [FeaturesValidation] Bond 3 of dative type is not allowed -194: Range Error -194: idx -194: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -194: Failed Expression: 12 < 6 -194: ---------- -194: Stacktrace: -194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -194: 4# 0x00007FC6DA481CE0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 6# 0x00007FC6DC9CB66C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so -194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -194: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x00007FC6DA3B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x00007FC6DA3B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x00007FC6DA3B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x00007FC6DA3B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 21# 0x00007FC6DA3B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -194: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -194: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 27# 0x00007FC6DC9C8406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 28# _PyObject_MakeTpCall in /usr/bin/python3 -194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 30# 0x00000000005BEE79 in /usr/bin/python3 -194: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 32# 0x0000000000547080 in /usr/bin/python3 -194: 33# 0x00000000006AB720 in /usr/bin/python3 -194: 34# _PyObject_MakeTpCall in /usr/bin/python3 -194: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 36# 0x00000000005BEE79 in /usr/bin/python3 -194: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 38# 0x0000000000547080 in /usr/bin/python3 -194: 39# 0x00000000006AB720 in /usr/bin/python3 -194: 40# _PyObject_MakeTpCall in /usr/bin/python3 -194: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 42# 0x00000000005BEE79 in /usr/bin/python3 -194: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 44# 0x0000000000547080 in /usr/bin/python3 -194: 45# 0x00000000006AB720 in /usr/bin/python3 -194: 46# _PyObject_MakeTpCall in /usr/bin/python3 -194: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 48# 0x000000000059582E in /usr/bin/python3 -194: 49# _PyObject_MakeTpCall in /usr/bin/python3 -194: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 51# PyEval_EvalCode in /usr/bin/python3 -194: 52# 0x000000000066A861 in /usr/bin/python3 -194: 53# 0x000000000066670C in /usr/bin/python3 -194: 54# 0x000000000067F713 in /usr/bin/python3 -194: 55# 0x000000000067ECE3 in /usr/bin/python3 -194: 56# 0x000000000067EB1E in /usr/bin/python3 -194: 57# Py_RunMain in /usr/bin/python3 -194: 58# Py_BytesMain in /usr/bin/python3 -194: 59# 0x00007FC6DD3B3D68 in /lib/x86_64-linux-gnu/libc.so.6 -194: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -194: 61# _start in /usr/bin/python3 -194: ---------- -194: **** -194: -194: [12:01:02] non-ring atom 0 marked aromatic -194: [12:01:02] non-ring atom 0 marked aromatic -194: [12:01:02] -194: -194: **** 204: ERROR: [FeaturesValidation] Atom 2 with alias 'CF3' is not allowed 204: ERROR: [FeaturesValidation] Enhanced stereochemistry features are not allowed 204: ERROR: [StereoValidation] Atom 3 has both unknown and wedged/dashed stereo bonds. @@ -31560,225 +33375,397 @@ 204: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. 204: there 204: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. -151: 1077656726 -151: =============================================================================== -151: All tests passed (73 assertions in 3 test cases) -151: -194: Range Error -194: idx -194: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -194: Failed Expression: 12 < 6 -194: ---------- -194: Stacktrace: -194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -194: 4# 0x00007FC6DA481CE0 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 6# 0x00007FC6DC9CB66C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so -194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -194: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x00007FC6DA3B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x00007FC6DA3B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x00007FC6DA3B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x00007FC6DA3B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 21# 0x00007FC6DA3B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -194: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -194: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 27# 0x00007FC6DC9C8406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 28# _PyObject_MakeTpCall in /usr/bin/python3 -194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 30# 0x00000000005BEE79 in /usr/bin/python3 -194: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 32# 0x0000000000547080 in /usr/bin/python3 -194: 33# 0x00000000006AB720 in /usr/bin/python3 -194: 34# _PyObject_MakeTpCall in /usr/bin/python3 -194: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 36# 0x00000000005BEE79 in /usr/bin/python3 -194: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 38# 0x0000000000547080 in /usr/bin/python3 -194: 39# 0x00000000006AB720 in /usr/bin/python3 -194: 40# _PyObject_MakeTpCall in /usr/bin/python3 -194: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 42# 0x00000000005BEE79 in /usr/bin/python3 -194: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 44# 0x0000000000547080 in /usr/bin/python3 -194: 45# 0x00000000006AB720 in /usr/bin/python3 -194: 46# _PyObject_MakeTpCall in /usr/bin/python3 -194: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 48# 0x000000000059582E in /usr/bin/python3 -194: 49# _PyObject_MakeTpCall in /usr/bin/python3 -194: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 51# PyEval_EvalCode in /usr/bin/python3 -194: 52# 0x000000000066A861 in /usr/bin/python3 -194: 53# 0x000000000066670C in /usr/bin/python3 -194: 54# 0x000000000067F713 in /usr/bin/python3 -194: 55# 0x000000000067ECE3 in /usr/bin/python3 -194: 56# 0x000000000067EB1E in /usr/bin/python3 -194: 57# Py_RunMain in /usr/bin/python3 -194: 58# Py_BytesMain in /usr/bin/python3 -194: 59# 0x00007FC6DD3B3D68 in /lib/x86_64-linux-gnu/libc.so.6 -194: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -194: 61# _start in /usr/bin/python3 -194: ---------- -194: **** -194: -164/235 Test #205: molChargeTest .......................... Passed 0.23 sec +185/235 Test #204: molValidateTest ........................ Passed 0.19 sec +test 205 + Start 205: molChargeTest + +205: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest +205: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +205: Test timeout computed to be: 1500 +152: .............[09:21:34] Molecule does not have explicit Hs. Consider calling AddHs() +186/235 Test #205: molChargeTest .......................... Passed 0.45 sec test 206 Start 206: molTautomerTest 206: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 206: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 206: Test timeout computed to be: 1500 -165/235 Test #151: molAlignCatchTest ...................... Passed 5.98 sec +152: [09:21:35] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:21:35] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:21:35] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:21:35] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:21:35] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:21:35] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:21:35] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:21:35] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:21:35] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:21:35] Molecule does not have explicit Hs. Consider calling AddHs() +187/235 Test #202: molStandardizeTest ..................... Passed 6.86 sec test 207 Start 207: molStandardizeSmallTest 207: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest 207: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 207: Test timeout computed to be: 1500 -166/235 Test #204: molValidateTest ........................ Passed 0.26 sec +176: VS001: PASSED +176: VS002: PASSED +176: VS003: PASSED +176: VS004: PASSED +176: VS005: PASSED +176: VS006: PASSED +176: VS007: PASSED +176: VS008: PASSED +176: VS009: PASSED +176: VS010: PASSED +176: VS011: PASSED +176: VS012: PASSED +176: VS013: PASSED +176: VS014: PASSED +176: VS015: PASSED +176: VS016: PASSED +176: VS017: PASSED +176: VS018: PASSED +176: VS019: PASSED +176: VS020: PASSED +176: VS021: PASSED +176: VS022: PASSED +176: VS023: PASSED +176: VS024: PASSED +176: VS025: PASSED +176: VS026: PASSED +176: VS027: PASSED +176: VS028: PASSED +176: VS029: PASSED +176: VS030: PASSED +176: VS031: PASSED +176: VS032: PASSED +176: VS033: PASSED +176: VS034: PASSED +176: VS035: PASSED +176: VS036: PASSED +176: VS037: PASSED +176: VS038: PASSED +176: VS039: PASSED +176: VS040: PASSED +176: VS041: PASSED +176: VS042: PASSED +176: VS043: PASSED +176: VS044: PASSED +176: VS045: PASSED +176: VS046: PASSED +176: VS047: PASSED +176: VS048: PASSED +176: VS049: PASSED 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+176: VS100: PASSED +176: VS101: PASSED +176: VS102: PASSED +176: VS103: PASSED +176: VS104: PASSED +176: VS105: PASSED +176: VS106: PASSED +176: VS107: PASSED +176: VS108: PASSED +176: VS109: PASSED +176: VS110: PASSED +176: VS111: PASSED +176: VS112: PASSED +176: VS113: PASSED +176: VS114: PASSED +176: VS115: PASSED +176: VS116: PASSED +176: VS117: PASSED +176: VS118: PASSED +176: VS119: PASSED +176: VS120: PASSED +176: VS121: PASSED +176: VS122: PASSED +176: VS123: PASSED +176: VS124: PASSED +176: VS125: PASSED +176: VS126: PASSED +176: VS127: PASSED +176: VS128: PASSED +176: VS129: PASSED +176: VS130: PASSED +176: VS131: PASSED +176: VS132: PASSED +176: VS133: PASSED +176: VS134: PASSED +176: VS135: PASSED +176: VS136: PASSED +176: VS137: PASSED +176: VS138: PASSED +176: VS139: PASSED +176: VS140: PASSED +176: VS141: PASSED +176: VS142: PASSED +176: VS143: PASSED +176: VS144: PASSED +176: VS145: PASSED +176: VS146: PASSED +176: VS147: PASSED +176: VS148: PASSED +176: VS149: PASSED +176: VS150: PASSED +176: VS151: PASSED +176: VS152: PASSED +176: VS153: PASSED +176: VS154: PASSED +176: VS155: PASSED +176: VS156: PASSED +176: VS157: PASSED +176: VS158: PASSED +176: VS159: PASSED +176: VS160: PASSED +176: VS161: PASSED +176: VS162: PASSED +176: VS163: PASSED +176: VS164: PASSED +176: VS165: PASSED +176: VS166: PASSED +176: VS167: PASSED +176: VS168: PASSED +176: VS169: PASSED +176: VS170: PASSED +176: VS171: PASSED +176: VS172: PASSED +176: VS173: PASSED +176: VS174: PASSED +176: VS175: PASSED +176: VS176: PASSED +176: VS177: PASSED +176: VS178: PASSED +176: VS179: PASSED +176: VS180: PASSED +176: VS181: PASSED +176: VS182: PASSED +176: VS183: PASSED +176: VS184: PASSED +176: VS185: PASSED +176: VS186: PASSED +176: VS187: PASSED +176: VS188: PASSED +176: VS189: PASSED +176: VS190: PASSED +176: VS191: PASSED +176: VS192: PASSED +176: VS193: PASSED +176: VS194: PASSED +176: VS195: PASSED +176: VS196: PASSED +176: VS197: PASSED +176: VS198: PASSED +176: VS199: PASSED +176: VS200: PASSED +176: VS201: PASSED +176: VS202: PASSED +176: VS203: PASSED +176: VS204: PASSED +176: VS205: PASSED +176: VS206: PASSED +176: VS207: PASSED +176: VS208: PASSED +176: VS209: PASSED +176: VS210: PASSED +176: VS211: PASSED +176: VS212: PASSED +176: VS213: PASSED +176: VS214: PASSED +176: VS215: PASSED +176: VS216: PASSED +176: VS217: PASSED +176: VS218: PASSED +176: VS219: PASSED +176: VS220: PASSED +176: VS221: PASSED +176: VS222: PASSED +176: VS223: PASSED +176: VS224: PASSED +176: VS225: PASSED +176: VS226: PASSED +176: VS227: PASSED +176: VS228: PASSED +176: VS229: PASSED +176: VS230: PASSED +176: VS231: PASSED +176: VS232: PASSED +176: VS233: PASSED +176: VS234: PASSED +176: VS235: PASSED +176: VS236: PASSED +176: VS237: PASSED +176: VS238: PASSED +176: VS239: PASSED +176: VS240: PASSED +176: VS241: PASSED +176: VS242: PASSED +176: VS243: PASSED +176: VS244: PASSED +176: VS245: PASSED +176: VS246: PASSED +176: VS247: PASSED +176: VS248: PASSED +176: VS249: PASSED +176: VS250: PASSED +176: VS251: PASSED +176: VS252: PASSED +176: VS253: PASSED +176: VS254: PASSED +176: VS255: PASSED +176: VS256: PASSED +176: VS257: PASSED +176: VS258: PASSED +176: VS259: PASSED +176: VS260: PASSED +176: VS261: PASSED +176: VS262: PASSED +176: VS263: PASSED +176: VS264: PASSED +176: VS265: PASSED +176: VS266: PASSED +176: VS267: PASSED +176: VS268: PASSED +176: VS269: PASSED +176: VS270: PASSED +176: VS271: PASSED +176: VS272: PASSED +176: VS273: PASSED +176: VS274: PASSED +176: VS275: PASSED +176: VS276: PASSED +176: VS277: PASSED +176: VS278: PASSED +176: VS279: PASSED +176: VS280: PASSED +176: VS281: PASSED +176: VS282: PASSED +176: VS283: PASSED +176: VS284: PASSED +176: VS285: PASSED +176: VS286: PASSED +176: VS287: PASSED +176: VS288: PASSED +176: VS289: PASSED +176: VS290: PASSED +176: VS291: PASSED +176: VS292: PASSED +176: VS293: PASSED +176: VS294: PASSED +176: VS295: PASSED +176: VS296: PASSED +176: VS297: PASSED +176: VS298: PASSED +176: VS299: PASSED +176: VS300: PASSED +176: Check finished: 0 molecules failed. +176: Failed: +188/235 Test #207: molStandardizeSmallTest ................ Passed 0.17 sec test 208 Start 208: molFragmentTest 208: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 208: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 208: Test timeout computed to be: 1500 -167/235 Test #200: pyTestPropertyLists .................... Passed 1.01 sec +189/235 Test #176: pyCIPLabelsValidation .................. Passed 28.07 sec test 209 Start 209: molStandardizeCatchTest 209: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 209: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 209: Test timeout computed to be: 1500 -168/235 Test #172: pyRascalMCES ........................... Passed 4.91 sec +208: [09:21:38] SMARTS Parse Error: syntax error while parsing: [Cl +208: [09:21:38] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +190/235 Test #208: molFragmentTest ........................ Passed 0.28 sec test 210 Start 210: molStandardizePipelineTest 210: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest 210: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 210: Test timeout computed to be: 1500 -188: .................... -188: ---------------------------------------------------------------------- -188: Ran 20 tests in 1.764s -188: -188: OK -169/235 Test #207: molStandardizeSmallTest ................ Passed 0.09 sec -test 211 - Start 211: pyMolStandardize - -211: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" -211: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap -211: Test timeout computed to be: 1500 -194: ...............[12:01:03] 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. -194: [12:01:03] 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. -143: [12:01:03] done -143: [12:01:03] ------------------------------------- -143: [12:01:03] Testing GitHubIssue62. -143: [12:01:03] beta-lactam 39.6387 -143: [12:01:03] cyclopropanone 174.698 -203: [12:01:03] Initializing Normalizer -203: [12:01:03] Running Normalizer -203: [12:01:03] Rule applied: BrokenazidetoN=N+=N- -143: [12:01:03] aziridine 337.986 -143: [12:01:03] aziridinone 115.248 -143: [12:01:03] isobutene 2.48217 -208: [12:01:03] SMARTS Parse Error: syntax error while parsing: [Cl -208: [12:01:03] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -210: Randomness seeded to: 2754184933 +210: Randomness seeded to: 3467529042 210: 1 Counts line too short: '' on line4 210: 1 Could not instantiate a valid molecule from input -170/235 Test #188: pyRGroupDecomposition .................. Passed 2.55 sec -test 212 - Start 212: testScaffoldNetwork - -212: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork -212: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork -212: Test timeout computed to be: 1500 -171/235 Test #208: molFragmentTest ........................ Passed 0.14 sec -test 213 - Start 213: pyScaffoldNetwork - -213: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" -213: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -213: Test timeout computed to be: 1500 -203: [12:01:03] Initializing Normalizer -203: [12:01:03] Running Normalizer -203: [12:01:03] Initializing Normalizer -203: [12:01:03] Running Normalizer -143: [12:01:03] acetone 1.91788 -172/235 Test #203: molNormalizeTest ....................... Passed 0.58 sec -test 214 - Start 214: pyScaffoldNetworkPickling - -214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" -214: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -214: Test timeout computed to be: 1500 -143: [12:01:03] cyclopentanone 10.1648 -143: [12:01:03] cyclopropene 99.4921 -143: [12:01:03] cyclobutene 41.0156 -143: [12:01:03] cyclopropane 267.236 210: 8 Molecule has no atoms -210: [12:01:03] Explicit valence for atom # 1 N, 4, is greater than permitted -210: [12:01:03] Explicit valence for atom # 1 N, 4, is greater than permitted -143: [12:01:03] gamma-lactam 15.7471 +210: [09:21:38] Explicit valence for atom # 1 N, 4, is greater than permitted +210: [09:21:38] Explicit valence for atom # 1 N, 4, is greater than permitted 210: 8 Explicit valence for atom # 1 N, 4, is greater than permitted 210: 128 An error occurred while preparing the molecule for standardization. 210: 8 The molecule contains an unknown isotope: 3C 210: 4 Query atom 0 is not allowed -160: file testGithub4323_3.png gave hash 4270327094U not the expected 381907253U 210: 4 Bond 0 of aromatic type is not allowed 210: 4 Bond 1 of aromatic type is not allowed 210: 4 Bond 2 of aromatic type is not allowed 210: 4 Bond 3 of aromatic type is not allowed 210: 4 Bond 5 of aromatic type is not allowed 210: 4 Bond 6 of aromatic type is not allowed -143: [12:01:03] trans-2,3-diphenylcyclopropan-1-one 203.398 -160: [12:01:03] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 210: 4 Bond 2 of dative type is not allowed 210: 4 Bond 3 of dative type is not allowed 210: 4 Enhanced stereochemistry features are not allowed 210: 8 The radical at atom 0 is not allowed -210: [12:01:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +210: [09:21:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 210: 16 The molecule includes non-null Z coordinates 210: 32 Atom 0 too close to bond 2 -194: ..............[12:01:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -194: [12:01:03] Explicit valence for atom # 1 C, 5, is greater than permitted 210: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit -143: [12:01:03] cis-2,3-diphenylcyclopropan-1-one 206.852 +206: [09:21:38] Tautomer enumeration stopped at 292 tautomers: max transforms reached 210: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 8.257s -12: -12: OK 210: 64 Atom 0 has adjacent stereo bonds with like orientation -210: [12:01:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +210: [09:21:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 210: 16 The molecule includes non-null Z coordinates 210: 64 Atom 0 has adjacent stereo bonds with like orientation -201: . -201: ---------------------------------------------------------------------- -201: Ran 1 test in 0.045s -201: -201: OK -143: [12:01:03] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 210: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit 210: 8388608 One or more metal atoms were disconnected. 210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 210: 67108864 The protonation state was adjusted. -143: [12:01:03] cyclopropylidencyclobutane 218.879 210: 16777216 The representation of some functional groups was adjusted. 210: 67108864 The protonation state was adjusted. 210: 16777216 The representation of some functional groups was adjusted. @@ -31788,45 +33775,13 @@ 210: 67108864 The protonation state was adjusted. 210: 16777216 The representation of some functional groups was adjusted. 210: 67108864 The protonation state was adjusted. -173/235 Test #12: pyBV ................................... Passed 8.91 sec -test 215 - Start 215: testMolEnumerator - -215: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator -215: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator -215: Test timeout computed to be: 1500 -143: [12:01:03] diphenylmethylidencyclobutane 79.6139 -143: [12:01:03] done -143: [12:01:03] ------------------------------------- -143: [12:01:03] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -143: [12:01:03] done -143: [12:01:03] ------------------------------------- -143: [12:01:03] Test square planar complexes -143: [12:01:03] done -143: [12:01:03] ------------------------------------- -143: [12:01:03] Test octahedral complexes -143: [12:01:03] done 210: 16777216 The representation of some functional groups was adjusted. 210: 67108864 The protonation state was adjusted. -174/235 Test #143: testUFFForceFieldHelpers ............... Passed 7.08 sec -test 216 - Start 216: pyMolEnumerator - -216: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" -216: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap -216: Test timeout computed to be: 1500 210: 16777216 The representation of some functional groups was adjusted. 210: 67108864 The protonation state was adjusted. 210: 8388608 One or more metal atoms were disconnected. 210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 210: 67108864 The protonation state was adjusted. -175/235 Test #201: pyCDXMLTest ............................ Passed 1.44 sec -test 217 - Start 217: testAbbreviations - -217: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations -217: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations -217: Test timeout computed to be: 1500 210: 8388608 One or more metal atoms were disconnected. 210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 210: 67108864 The protonation state was adjusted. @@ -31836,2090 +33791,155 @@ 210: 8388608 One or more metal atoms were disconnected. 210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 210: 67108864 The protonation state was adjusted. -215: Randomness seeded to: 1170728927 -215: [12:01:03] can only enumerate SRUs with CONNECT=HT or CONNECT=HH 210: 8388608 One or more metal atoms were disconnected. 210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. 210: 67108864 The protonation state was adjusted. -217: Randomness seeded to: 3317247131 -217: [12:01:03] SMARTS Parse Error: syntax error while parsing: *fail -217: [12:01:03] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' 210: 16777216 The "wavy" style of bond 4 was removed 210: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration 210: 16777216 The "wavy" style of bond 2 was removed -217: [12:01:03] no suitable SubstanceGroups found -217: =============================================================================== -217: All tests passed (195 assertions in 12 test cases) -217: 210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 210: 16777216 The "wavy" style of bond 1 was removed -176/235 Test #217: testAbbreviations ...................... Passed 0.10 sec -test 218 - Start 218: pyAbbreviations - -218: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" -218: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap -218: Test timeout computed to be: 1500 210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 210: 16777216 The "wavy" style of bond 1 was removed 210: 16777216 The "wavy" style of bond 4 was removed -215: =============================================================================== -215: All tests passed (321 assertions in 16 test cases) -215: 210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration 210: 16777216 The "wavy" style of bond 3 was removed -209: Randomness seeded to: 156552947 -209: * - * - * - * m1 -177/235 Test #215: testMolEnumerator ...................... Passed 0.23 sec -test 219 - Start 219: generalizedSubstructCatch - -219: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch -219: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct -219: Test timeout computed to be: 1500 -209: * - * - * - * m2 210: 16777216 The representation of some functional groups was adjusted. -214: . -214: ---------------------------------------------------------------------- -214: Ran 1 test in 0.031s -214: -214: OK -209: * - * - * - * m1 -210: [12:01:03] Can't kekulize mol. Unkekulized atoms: 2 3 5 -209: * - * - * - * m2 +210: [09:21:38] Can't kekulize mol. Unkekulized atoms: 2 3 5 210: =============================================================================== 210: All tests passed (268 assertions in 5 test cases) 210: -178/235 Test #210: molStandardizePipelineTest ............. Passed 0.77 sec -test 220 - Start 220: pyGeneralizedSubstruct +191/235 Test #210: molStandardizePipelineTest ............. Passed 0.45 sec +test 211 + Start 211: pyMolStandardize -220: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" -220: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap -220: Test timeout computed to be: 1500 +211: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" +211: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap +211: Test timeout computed to be: 1500 +209: Randomness seeded to: 1480957486 +209: * - * - * - * m1 +209: * - * - * - * m2 +209: * - * - * - * m1 +209: * - * - * - * m2 +209: [09:21:39] Can't kekulize mol. Unkekulized atoms: 3 7 +209: [09:21:39] Can't kekulize mol. Unkekulized atoms: 3 8 +209: [09:21:39] Can't kekulize mol. Unkekulized atoms: 2 3 4 +211: .....[09:21:40] Tautomer enumeration stopped at 292 tautomers: max transforms reached +211: [09:21:40] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +182: [09:21:40] ------------------------------------- +182: [09:21:40] Results do not depend on numThreads (all same) +206: [09:21:40] Tautomer enumeration stopped at 292 tautomers: max transforms reached +182: [09:21:40] ------------------------------------- +182: [09:21:40] testTautomerQueries +182: [09:21:40] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +182: [09:21:40] ------------------------------------- +182: [09:21:40] github3881 recursive smarts with rings +211: .[09:21:40] Tautomer enumeration stopped at 40 tautomers: canceled +211: Enumeration was canceled due to timeout (50 ms) +192/235 Test #182: substructLibraryTest ................... Passed 27.11 sec +test 212 + Start 212: testScaffoldNetwork + +212: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork +212: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork +212: Test timeout computed to be: 1500 +206: [09:21:40] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +206: [09:21:41] Tautomer enumeration stopped at 30 tautomers: canceled +206: Enumeration was canceled due to timeout (50 ms) +173: Query 0 +152: ...[09:21:44] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:21:44] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:21:44] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:21:44] Molecule does not have explicit Hs. Consider calling AddHs() +152: [09:21:44] Molecule does not have explicit Hs. Consider calling AddHs() +152: ... +152: ---------------------------------------------------------------------- +152: Ran 19 tests in 60.293s +152: +152: OK +152: Testing MolAlign Wrappers +206: 375 +206: Enumeration has completed +193/235 Test #152: pyMolAlign ............................. Passed 61.07 sec +test 213 + Start 213: pyScaffoldNetwork + +213: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" +213: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +213: Test timeout computed to be: 1500 +29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +206: [09:21:44] Tautomer enumeration stopped at 23 tautomers: canceled +211: Enumeration has completed +211: [09:21:44] Tautomer enumeration stopped at 19 tautomers: canceled +29: All 191 tests passed +29: done +29: ------------------------------------- +29: Unit tests for all MMFF constraint terms. +29: 10.0003 +29: done +29: ------------------------------------- +29: Unit test for MMFF TorsionConstraint close to 0 degrees. +29: done +29: ------------------------------------- +29: Unit tests for copying MMFF ForceFields. +29: done +29: ------------------------------------- +29: Unit test for MMFF butane scan. 213: ....... 213: ---------------------------------------------------------------------- -213: Ran 7 tests in 0.055s +213: Ran 7 tests in 0.056s 213: 213: OK -209: [12:01:03] Can't kekulize mol. Unkekulized atoms: 3 7 -209: [12:01:03] Can't kekulize mol. Unkekulized atoms: 3 8 -209: [12:01:03] Can't kekulize mol. Unkekulized atoms: 2 3 4 -169: ......... -169: ---------------------------------------------------------------------- -169: Ran 9 tests in 5.215s -169: -169: OK -179/235 Test #213: pyScaffoldNetwork ...................... Passed 0.72 sec -test 221 - Start 221: testMolProcessing - -221: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing -221: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing -221: Test timeout computed to be: 1500 -180/235 Test #214: pyScaffoldNetworkPickling .............. Passed 0.74 sec -test 222 - Start 222: pyMolProcessing - -222: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" -222: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap -222: Test timeout computed to be: 1500 -181/235 Test #169: pyMMPA ................................. Passed 6.11 sec -test 223 - Start 223: testMIF - -223: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF -223: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields -223: Test timeout computed to be: 1500 -160: file testFlexiCanvas.2a.png gave hash 2907977766U not the expected 2609920321U -160: file testFlexiCanvas.2b.png gave hash 1585391483U not the expected 3615599154U -160: file testFlexiCanvas.3.svg gave hash 236661785U not the expected 3544316588U -223: Randomness seeded to: 3651347952 -223: =============================================================================== -223: All tests passed (27926 assertions in 8 test cases) -223: -182/235 Test #223: testMIF ................................ Passed 0.19 sec -test 224 - Start 224: pyMIF - -224: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" -224: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap -224: Test timeout computed to be: 1500 -160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U -160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U -160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U -160: file testGithub4764.sz1.png gave hash 1417438968U not the expected 2179222277U -160: file testGithub4764.sz2.png gave hash 2455997703U not the expected 444262090U -194: ............................[12:01:04] unable to set wavy bonds for double bonds: 3 -218: ....... -218: ---------------------------------------------------------------------- -218: Ran 7 tests in 0.053s -218: -218: OK -148: [12:01:04] Molecule does not have explicit Hs. Consider calling AddHs() -194: .............[12:01:04] -194: -194: **** -194: Range Error -194: idx -194: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -194: Failed Expression: 6 < 5 -194: ---------- -194: Stacktrace: -194: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -194: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 6# 0x00007FC6DC9CB66C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -194: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -194: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -194: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so -194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -194: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x00007FC6DA3B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x00007FC6DA3B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x00007FC6DA3B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x00007FC6DA3B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 21# 0x00007FC6DA3B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -194: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -194: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 27# 0x00007FC6DC9C8406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 28# _PyObject_MakeTpCall in /usr/bin/python3 -194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 30# 0x00000000005BEE79 in /usr/bin/python3 -194: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 32# 0x0000000000547080 in /usr/bin/python3 -194: 33# 0x00000000006AB720 in /usr/bin/python3 -194: 34# _PyObject_MakeTpCall in /usr/bin/python3 -194: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 36# 0x00000000005BEE79 in /usr/bin/python3 -194: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 38# 0x0000000000547080 in /usr/bin/python3 -194: 39# 0x00000000006AB720 in /usr/bin/python3 -194: 40# _PyObject_MakeTpCall in /usr/bin/python3 -194: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 42# 0x00000000005BEE79 in /usr/bin/python3 -194: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 44# 0x0000000000547080 in /usr/bin/python3 -194: 45# 0x00000000006AB720 in /usr/bin/python3 -194: 46# _PyObject_MakeTpCall in /usr/bin/python3 -194: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 48# 0x000000000059582E in /usr/bin/python3 -194: 49# _PyObject_MakeTpCall in /usr/bin/python3 -194: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -194: 51# PyEval_EvalCode in /usr/bin/python3 -194: 52# 0x000000000066A861 in /usr/bin/python3 -194: 53# 0x000000000066670C in /usr/bin/python3 -194: 54# 0x000000000067F713 in /usr/bin/python3 -194: 55# 0x000000000067ECE3 in /usr/bin/python3 -194: 56# 0x000000000067EB1E in /usr/bin/python3 -194: 57# Py_RunMain in /usr/bin/python3 -194: 58# Py_BytesMain in /usr/bin/python3 -194: 59# 0x00007FC6DD3B3D68 in /lib/x86_64-linux-gnu/libc.so.6 -194: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -194: 61# _start in /usr/bin/python3 -194: ---------- -194: **** -194: -160: file testGithub4764.sz3.png gave hash 182513311U not the expected 3567162200U -216: ... -216: ---------------------------------------------------------------------- -216: Ran 3 tests in 0.049s -216: -216: OK -183/235 Test #218: pyAbbreviations ........................ Passed 0.88 sec -test 225 - Start 225: testQuery - -225: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Query/testQuery -225: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Query -225: Test timeout computed to be: 1500 -225: Query -225: Query2 -225: Equality -225: Greater -225: GreaterEqual -225: Less -225: LessEqual -225: Open Range -225: Closed Range -225: Float -225: With Tolerance -225: Set -225: And -225: Or -225: XOr -225: pointer and copy foo -225: Set2 -184/235 Test #225: testQuery .............................. Passed 0.01 sec -test 226 - Start 226: testBaseFeatures - -226: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Features/testBaseFeatures -226: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Features -226: Test timeout computed to be: 1500 -160: file github5383_1.svg gave hash 4241964660U not the expected 1815941817U -160: file github5383_2.svg gave hash 2560846108U not the expected 0U -226: ------------------------------------- -226: Basics for ExplicitFeatures. -226: done -226: ------------------------------------- -226: Basics for ImplicitFeatures. -226: done -226: ------------------------------------- -226: ExplicitFeatures 2D, string type. -226: done -185/235 Test #226: testBaseFeatures ....................... Passed 0.02 sec -test 227 - Start 227: testMatCalc - -227: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc -227: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc -227: Test timeout computed to be: 1500 -227: 1.68022e+08 -227: 1.73149e+08 -227: 1.05549e+08 -227: 7.20603e+07 -227: 1.41535e+08 -227: 1.08592e+08 -227: 1.11334e+08 -227: 2.05553e+08 -227: 1.54962e+08 -227: 8.08231e+07 -227: 5.61421e+07 -227: 1.28874e+08 -227: 1.59011e+08 -227: 8.69902e+07 -227: 1.31367e+08 -227: 2.27389e+08 -227: 1.60289e+08 -227: 7.79813e+07 -227: 1.61001e+08 -227: 2.07599e+08 -227: 2.24432e+08 -227: 1.39725e+08 -227: 2.42614e+08 -227: 1.77578e+08 -227: 1.05908e+08 -227: 9.06742e+07 -227: 1.8087e+08 -227: 1.98182e+08 -227: 2.03052e+08 -227: 1.7673e+08 -227: 9.32798e+07 -227: 1.37969e+08 -227: 1.83778e+08 -227: 2.1228e+08 -227: 5.06157e+07 -227: 1.566e+08 -227: 2.37142e+08 -227: 1.49345e+08 -227: 7.05819e+07 -227: 1.71633e+08 -227: 1.96817e+08 -227: 2.18246e+08 -227: 9.49496e+07 -227: 2.25618e+08 -227: 1.30219e+08 -186/235 Test #227: testMatCalc ............................ Passed 0.02 sec -test 228 - Start 228: pyMatCalc - -228: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" -228: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap -228: Test timeout computed to be: 1500 -160: file github5383_1.png gave hash 53778753U not the expected 2893520928U -160: file acs1996_1.png gave hash 1997633690U not the expected 2329725800U -219: Randomness seeded to: 867618766 -219: =============================================================================== -219: All tests passed (486 assertions in 10 test cases) -219: -160: file acs1996_2.png gave hash 3378065352U not the expected 2996350718U -160: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U -187/235 Test #219: generalizedSubstructCatch .............. Passed 0.94 sec -test 229 - Start 229: testSimDivPickers - -229: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers/testSimDivPickers -229: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers -229: Test timeout computed to be: 1500 -229: [12:01:04] ------------------------------------- -229: [12:01:04] Testing github issue 1421: MaxMinPicker picking non-existent element. -229: [12:01:04] Done -229: [12:01:04] ------------------------------------- -229: [12:01:04] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -229: [12:01:04] Done -188/235 Test #229: testSimDivPickers ...................... Passed 0.02 sec -test 230 - Start 230: pickersTestsCatch - -230: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers/pickersTestsCatch -230: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers -230: Test timeout computed to be: 1500 -189/235 Test #216: pyMolEnumerator ........................ Passed 1.19 sec -test 231 - Start 231: pySimDivPickers - -231: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/Wrap/testPickers.py" -231: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap -231: Test timeout computed to be: 1500 -160: [12:01:04] 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 3610726614U not the expected 3119784980U -190/235 Test #43: resMolSupplierTest ..................... Passed 10.01 sec -test 232 - Start 232: pyRanker - -232: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/Wrap/testRanker.py" -232: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap -232: Test timeout computed to be: 1500 -148: [12:01:04] Molecule does not have explicit Hs. Consider calling AddHs() -220: ....... -220: ---------------------------------------------------------------------- -220: Ran 7 tests in 0.443s -220: -220: OK -230: Randomness seeded to: 3216303135 -230: =============================================================================== -230: All tests passed (21267 assertions in 1 test case) -230: -191/235 Test #230: pickersTestsCatch ...................... Passed 0.26 sec -test 233 - Start 233: testChemicalFeatures - -233: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures -233: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures -233: Test timeout computed to be: 1500 -233: ----------------------------------------- -233: Test1 -233: Done -192/235 Test #233: testChemicalFeatures ................... Passed 0.02 sec -test 234 - Start 234: pyFeatures - -234: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/Wrap/testFeatures.py" -234: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap -234: Test timeout computed to be: 1500 -160: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U -193/235 Test #220: pyGeneralizedSubstruct ................. Passed 1.23 sec -test 235 - Start 235: pythonProjectTests +194/235 Test #213: pyScaffoldNetwork ...................... Passed 0.88 sec +test 214 + Start 214: pyScaffoldNetworkPickling -235: Test command: /usr/bin/python3 "-m" "pytest" -235: Working Directory: /build/reproducible-path/rdkit-202409.6/Projects -235: Test timeout computed to be: 1500 -206: [12:01:05] Tautomer enumeration stopped at 292 tautomers: max transforms reached -224: ....... -224: ---------------------------------------------------------------------- -224: Ran 7 tests in 0.180s -224: -224: OK -224: Testing MIF wrapper -148: [12:01:05] Molecule does not have explicit Hs. Consider calling AddHs() -222: .. -222: ---------------------------------------------------------------------- -222: Ran 2 tests in 0.732s -222: -222: OK -194/235 Test #224: pyMIF .................................. Passed 1.14 sec -148: [12:01:05] Molecule does not have explicit Hs. Consider calling AddHs() -232: ..[12:01:05] -232: -232: **** -232: Invariant Violation -232: Can't rank more bits than the ensemble size -232: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp -232: Failed Expression: num <= dp_maskBits->getNumOnBits() -232: ---------- -232: Stacktrace: -232: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -232: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -232: 2# RDInfoTheory::InfoBitRanker::getTopN(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitInfoTheory.so.1 -232: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so -232: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so -232: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -232: 6# 0x00007FB64179166C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -232: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -232: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -232: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -232: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -232: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so -232: 12# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -232: 13# 0x00007FB64178E406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -232: 14# _PyObject_MakeTpCall in /usr/bin/python3 -232: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 -232: 16# 0x00000000005BEE79 in /usr/bin/python3 -232: 17# _PyEval_EvalFrameDefault in /usr/bin/python3 -232: 18# 0x0000000000547080 in /usr/bin/python3 -232: 19# 0x00000000006AB720 in /usr/bin/python3 -232: 20# _PyObject_MakeTpCall in /usr/bin/python3 -232: 21# _PyEval_EvalFrameDefault in /usr/bin/python3 -232: 22# 0x00000000005BEE79 in /usr/bin/python3 -232: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 -232: 24# 0x0000000000547080 in /usr/bin/python3 -232: 25# 0x00000000006AB720 in /usr/bin/python3 -232: 26# _PyObject_MakeTpCall in /usr/bin/python3 -232: 27# _PyEval_EvalFrameDefault in /usr/bin/python3 -232: 28# 0x00000000005BEE79 in /usr/bin/python3 -232: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -232: 30# 0x0000000000547080 in /usr/bin/python3 -232: 31# 0x00000000006AB720 in /usr/bin/python3 -232: 32# _PyObject_MakeTpCall in /usr/bin/python3 -232: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 -232: 34# 0x000000000059582E in /usr/bin/python3 -232: 35# _PyObject_MakeTpCall in /usr/bin/python3 -232: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 -232: 37# PyEval_EvalCode in /usr/bin/python3 -232: 38# 0x000000000066A861 in /usr/bin/python3 -232: 39# 0x000000000066670C in /usr/bin/python3 -232: 40# 0x000000000067F713 in /usr/bin/python3 -232: 41# 0x000000000067ECE3 in /usr/bin/python3 -232: 42# 0x000000000067EB1E in /usr/bin/python3 -232: 43# Py_RunMain in /usr/bin/python3 -232: 44# Py_BytesMain in /usr/bin/python3 -232: 45# 0x00007FB642E14D68 in /lib/x86_64-linux-gnu/libc.so.6 -232: 46# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -232: 47# _start in /usr/bin/python3 -232: ---------- -195/235 Test #222: pyMolProcessing ........................ Passed 1.52 sec -232: **** -232: -232: ... -232: ---------------------------------------------------------------------- -232: Ran 5 tests in 0.044s -232: -232: OK -160: file AtropManyChiralsEnhanced.svg gave hash 3443464321U not the expected 2256768013U -231: [12:01:05] the useCache argument is deprecated and ignored -196/235 Test #232: pyRanker ............................... Passed 0.69 sec -148: [12:01:05] Molecule does not have explicit Hs. Consider calling AddHs() -211: .....[12:01:05] Tautomer enumeration stopped at 292 tautomers: max transforms reached -185: iterative -160: file testGithub_7739_1.svg gave hash 3358510977U not the expected 2615562225U -160: file testGithub_7739_3.svg gave hash 176211825U not the expected 1037942338U -160: file testGithub_7739_4.svg gave hash 3309264286U not the expected 3549083171U -160: [12:01:05] -160: -160: **** -160: Pre-condition Violation -160: -160: Violation occurred on line 206 in file ./Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp -160: Failed Expression: atomIdx < atCds_.size() && atomIdx < atomLabels_.size() -160: ---------- -160: Stacktrace: -160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -160: 2# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::calcSymbolEllipse(unsigned int, RDGeom::Point2D&, double&, double&) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeAtomHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 8# 0x000055A864A90DF5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 9# 0x000055A864B72A88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 10# 0x000055A864B735A8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 11# 0x000055A864B73A20 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 12# 0x000055A864B455C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 13# 0x000055A864B4592C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 14# 0x000055A864A8956E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 15# 0x00007FAD98E33D68 in /lib/x86_64-linux-gnu/libc.so.6 -160: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -160: 17# 0x000055A864A895B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: ---------- -160: **** -160: -160: [12:01:05] -160: -160: **** -160: Range Error -160: idx -160: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp -160: Failed Expression: 2 < 0 -160: ---------- -160: Stacktrace: -160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -160: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 8# 0x000055A864A90562 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 9# 0x000055A864B72A88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 10# 0x000055A864B735A8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 11# 0x000055A864B73A20 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 12# 0x000055A864B455C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 13# 0x000055A864B4592C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 14# 0x000055A864A8956E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 15# 0x00007FAD98E33D68 in /lib/x86_64-linux-gnu/libc.so.6 -160: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -160: 17# 0x000055A864A895B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: ---------- -160: **** -160: -160: [12:01:05] -160: -160: **** -160: Range Error -160: idx -160: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp -160: Failed Expression: 0 < 0 -160: ---------- -160: Stacktrace: -160: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -160: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -160: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -160: 3# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::makeBondHighlights(std::vector >, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 4# RDKit::MolDraw2D_detail::DrawMolMCHCircleAndLine::extractMCHighlights() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 8# 0x000055A864A90EC8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 9# 0x000055A864B72A88 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 10# 0x000055A864B735A8 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 11# 0x000055A864B73A20 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 12# 0x000055A864B455C3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 13# 0x000055A864B4592C in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 14# 0x000055A864A8956E in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 15# 0x00007FAD98E33D68 in /lib/x86_64-linux-gnu/libc.so.6 -160: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -160: 17# 0x000055A864A895B1 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: ---------- -231: ...[12:01:05] the useCache argument is deprecated and ignored -231: [12:01:05] the useCache argument is deprecated and ignored -160: **** -160: -231: .[12:01:05] the useCache argument is deprecated and ignored -160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U -146: validating reference data -148: [12:01:05] Molecule does not have explicit Hs. Consider calling AddHs() -197/235 Test #202: molStandardizeTest ..................... Passed 3.45 sec -211: [12:01:05] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -128: [12:01:05] done -128: [12:01:05] ------------------------------------- -128: [12:01:05] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -128: [12:01:05] done -128: [12:01:05] ------------------------------------- -128: [12:01:05] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -128: [12:01:05] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:01:05] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] done -128: [12:01:05] ------------------------------------- -128: [12:01:05] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -128: [12:01:05] done -128: [12:01:05] ------------------------------------- -128: [12:01:05] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] done -128: [12:01:05] ------------------------------------- -128: [12:01:05] Test unfolded version of RDKFP -128: [12:01:05] ------------------------------------- -128: [12:01:05] 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: [12:01:05] ------------------------------------- -128: [12:01:05] Single atoms setting radius 1 bits in Morgan fingerprints -128: [12:01:05] done -128: [12:01:05] ------------------------------------- -128: [12:01:05] Github #879: Pattern fingerprint should set bits for single-atom fragments. -128: [12:01:05] done -128: [12:01:05] ------------------------------------- -128: [12:01:05] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -128: [12:01:05] done -128: [12:01:05] ------------------------------------- -128: [12:01:05] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -128: [12:01:05] done -128: [12:01:05] ------------------------------------- -128: [12:01:05] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -128: [12:01:05] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:01:05] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:01:05] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:01:05] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:01:05] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:01:05] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:01:05] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:01:05] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:01:05] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:01:05] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:01:05] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:01:05] DEPRECATION WARNING: please use AtomPairGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [12:01:05] done -128: [12:01:05] ------------------------------------- -128: [12:01:05] Github #2115: BitInfo not complete for RDKFingerprint -128: [12:01:05] done -128: [12:01:05] ------------------------------------- -128: [12:01:05] Github #3723: Fingerprint crash for mols with Zero order bonds -128: [12:01:05] done -160: =============================================================================== -160: All tests passed (6853 assertions in 115 test cases) -160: -206: [12:01:05] Tautomer enumeration stopped at 292 tautomers: max transforms reached -198/235 Test #160: moldraw2DTestCatch ..................... Passed 8.69 sec -199/235 Test #128: testFingerprints ....................... Passed 9.96 sec -234: .. -234: ---------------------------------------------------------------------- -234: Ran 2 tests in 0.007s -234: -234: OK -234: Testing ChemicalFeatures Wrapper code: -206: [12:01:06] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -29: All 191 tests passed -200/235 Test #234: pyFeatures ............................. Passed 1.20 sec -212: Randomness seeded to: 2084924489 +214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" +214: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +214: Test timeout computed to be: 1500 +212: Randomness seeded to: 2720259112 212: =============================================================================== 212: All tests passed (273 assertions in 19 test cases) 212: -201/235 Test #212: testScaffoldNetwork .................... Passed 3.15 sec -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 -206: [12:01:06] Tautomer enumeration stopped at 71 tautomers: canceled -206: Enumeration was canceled due to timeout (50 ms) -185: bulk -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -163: [12:01:06] The provided InitialSeed is not an MCS and will be ignored -211: .[12:01:06] Tautomer enumeration stopped at 22 tautomers: canceled -211: Enumeration was canceled due to timeout (50 ms) -228: ..... -228: ---------------------------------------------------------------------- -228: Ran 5 tests in 1.093s -228: -228: OK -117: =>start test GETAWAY custom -117: [12:01:06] test on : 365 molecules done -202/235 Test #117: testRDFcustom .......................... Passed 11.14 sec -203/235 Test #228: pyMatCalc .............................. Passed 2.17 sec -171: Randomness seeded to: 3040348433 -171: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -194: ....................[12:01:07] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [12:01:07] Explicit valence for atom # 6 F, 2, is greater than permitted -194: [12:01:07] Can't kekulize mol. Unkekulized atoms: 3 4 5 -148: .[12:01:07] Molecule does not have explicit Hs. Consider calling AddHs() -194: .................[12:01:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -206: 375 -206: Enumeration has completed -231: ....... -231: ---------------------------------------------------------------------- -231: Ran 11 tests in 2.183s -231: -231: OK -204/235 Test #231: pySimDivPickers ........................ Passed 2.85 sec -206: [12:01:07] Tautomer enumeration stopped at 25 tautomers: canceled -150: processing -150: launch :0 -150: launch :1 -150: launch :2 -150: launch :3 -146: processing -146: launch :0 -146: launch :1 -146: launch :2 -146: launch :3 -125: Warning: Atom Count for residue GLU5A does not match expected count -125: Warning: Atom Count for residue ASN39A does not match expected count -125: Warning: Atom Count for residue GLU53A does not match expected count -125: Warning: Atom Count for residue ARG64A does not match expected count -125: Warning: Atom Count for residue LYS80A does not match expected count -125: Warning: Atom Count for residue GLU150A does not match expected count -125: Warning: Atom Count for residue ASN157A does not match expected count -125: =============================================================================== -125: All tests passed (515 assertions in 10 test cases) -125: -205/235 Test #125: descriptorsTestCatch ................... Passed 12.34 sec -235: ============================= test session starts ============================== -235: platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 -235: rootdir: /build/reproducible-path/rdkit-202409.6/Projects -235: configfile: pytest.ini -235: plugins: typeguard-4.4.2 -235: collected 12 items -235: -170: Randomness seeded to: 708810510 -170: [12:01:09] Timed out after 11 seconds. -164: ........................................[12:01:10] The provided InitialSeed is not an MCS and will be ignored -164: [12:01:10] The provided InitialSeed is not an MCS and will be ignored -164: [12:01:10] The provided InitialSeed is not an MCS and will be ignored -164: .[12:01:10] The provided InitialSeed is not an MCS and will be ignored -164: [12:01:10] The provided InitialSeed is not an MCS and will be ignored -164: [12:01:10] The provided InitialSeed is not an MCS and will be ignored -164: .[12:01:10] The provided InitialSeed is not an MCS and will be ignored -164: [12:01:10] The provided InitialSeed is not an MCS and will be ignored -164: [12:01:10] The provided InitialSeed is not an MCS and will be ignored -164: .[12:01:10] The provided InitialSeed is not an MCS and will be ignored -164: [12:01:10] The provided InitialSeed is not an MCS and will be ignored -164: [12:01:10] The provided InitialSeed is not an MCS and will be ignored -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 -164: ................. -164: ---------------------------------------------------------------------- -164: Ran 60 tests in 11.904s -164: -164: OK -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 -206/235 Test #164: pyFMCS ................................. Passed 12.85 sec -185: bulk, no symmetry -173: [12:01:10] Building the fingerprints may take some time. -126: .[12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: .[12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: ..[12:01:10] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:01:10] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:01:10] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:01:10] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:01:10] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:01:10] DEPRECATION WARNING: please use AtomPairGenerator -126: .[12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ...[12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: [12:01:10] DEPRECATION WARNING: please use MorganGenerator -126: ....[12:01:10] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:01:10] DEPRECATION WARNING: please use AtomPairGenerator -126: ....[12:01:10] DEPRECATION WARNING: please use AtomPairGenerator -126: [12:01:10] DEPRECATION WARNING: please use AtomPairGenerator -126: .[12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: .[12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [12:01:10] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ... -126: ---------------------------------------------------------------------- -126: Ran 31 tests in 13.346s -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 -207/235 Test #126: pyMolDescriptors ....................... Passed 14.64 sec -221: Randomness seeded to: 1630897159 -221: =============================================================================== -221: All tests passed (203 assertions in 1 test case) -221: -208/235 Test #221: testMolProcessing ...................... Passed 6.82 sec -211: Enumeration has completed -211: [12:01:10] Tautomer enumeration stopped at 23 tautomers: canceled -182: [12:01:11] ------------------------------------- -182: [12:01:11] testing PatternHolder -211: ..........[12:01:11] Explicit valence for atom # 1 N, 4, is greater than permitted -211: [12:01:11] Explicit valence for atom # 1 N, 4, is greater than permitted -211: [12:01:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -211: [12:01:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -185: [12:01:11] Relabelling existing label -182: [12:01:11] ------------------------------------- -182: [12:01:11] testing TautomerPatternHolder -206: CN=c1cc[nH]cn1 -206: CN=c1ccnc[nH]1 -206: CNc1ccncn1 -206: res: CNc1ccncn1 -206: CN=c1cccc[nH]1 -206: CNc1ccccn1 -206: res: CNc1ccccn1 -185: Best mapping -182: [12:01:12] ------------------------------------- -182: [12:01:12] testSegFaultInHolder -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] [12:01:12] ^ -182: SMILES Parse Error: syntax error while parsing: dsafsdf[12:01:12] [12:01:12] [12:01:12] [12:01:12] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf[12:01:12] -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: syntax error while parsing: : -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] [12:01:12] [12:01:12] SMILES Parse Error: SMILESdsafsdf Parse Error: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: SMILES Parse Error: [12:01:12] syntax error while parsing: dsafsdf -182: SMILES Parse Error: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^syntax error while parsing: syntax errordsafsdf -182: while parsing: dsafsdf -182: [12:01:12] syntax errorSMILES Parse Error: syntax error -182: [12:01:12] SMILES Parse Error: check for mistakes around position [12:01:12] 1 while parsing: for input: ' -182: [12:01:12] while parsing: SMILES Parse Error: check for mistakes around position 1:dsafsdf[12:01:12] dsafsdfSMILES Parse Error: check for mistakes around position ' -182: :SMILES Parse Error: check for mistakes around position -182: [12:01:12] dsafsdf1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf -182: -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1:[12:01:12] -182: SMILES1 for input: 'dsafsdf' -182: : -182: [12:01:12] SMILES Parse Error: check for mistakes around position [12:01:12] dsafsdf -182: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[12:01:12] '1: -182: dsafsdf[12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] -182: ^ -182: [12:01:12] dsafsdf -182: [12:01:12] ^[12:01:12] -182: SMILES Parse Error: -182: Failed parsing SMILES 'dsafsdf' for input: '[12:01:12] [12:01:12] dsafsdf -182: SMILES Parse Error: check for mistakes around position [12:01:12] 1[12:01:12] ^ -182: -182: dsafsdf' -182: ^ -182: [12:01:12] ^ -182: -182: [12:01:12] [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf': for input: 'dsafsdf' -182: -182: [12:01:12] for input: 'SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1dsafsdf' -182: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: : -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1[12:01:12] [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf[12:01:12] -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: [12:01:12] : -182: SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: SMILES Parse Error: syntax error while parsing: dsafsdf -182: SMILES Parse Error: syntax error while parsing: dsafsdf[12:01:12] SMILES Parse Error: check for mistakes around position -182: 1: -182: [12:01:12] dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[12:01:12] [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] [12:01:12] SMILESSMILES Parse Error: syntax error Parse Error: Failed parsing SMILES 'dsafsdf'[12:01:12] for input: 'dsafsdf'syntax errorSMILES Parse Error: while parsing: dsafsdf -182: syntax error while parsing: syntax error[12:01:12] while parsing: [12:01:12] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: for input: 'dsafsdf[12:01:12] -182: dsafsdfsyntax error while parsing: while parsing: [12:01:12] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: check for mistakes around position -182: ::dsafsdf11: -182: : -182: dsafsdf -182: [12:01:12] -182: SMILES Parse Error: check for mistakes around position dsafsdf1 -182: [12:01:12] dsafsdf[12:01:12] -182: -182: :[12:01:12] dsafsdf[12:01:12] SMILES Parse Error: check for mistakes around position -182: [12:01:12] [12:01:12] dsafsdf -182: '[12:01:12] [12:01:12] dsafsdfSMILES Parse Error: check for mistakes around position -182: [12:01:12] dsafsdf[12:01:12] 1[12:01:12] : -182: SMILES Parse Error: syntax error1^ -182: :^ -182: SMILES Parse Error: check for mistakes around position -182: -182: SMILES Parse Error: check for mistakes around position -182: -182: [12:01:12] -182: [12:01:12] 1[12:01:12] :[12:01:12] -182: ^[12:01:12] dsafsdf1dsafsdf: -182: -182: [12:01:12] ^[12:01:12] ^ -182: -182: [12:01:12] -182: dsafsdfSMILES -182: -182: SMILES[12:01:12] Parse Error: Parse Error: [12:01:12] Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: '[12:01:12] dsafsdf'[12:01:12] ^SMILES[12:01:12] Parse Error: [12:01:12] dsafsdf -182: for input: 'dsafsdf[12:01:12] SMILESFailed parsing SMILES 'dsafsdf'SMILES for input: ' -182: Parse Error: ' -182: dsafsdf -182: [12:01:12] 'dsafsdf -182: Failed parsing SMILES 'dsafsdf' -182: ^^ -182: for input: ' Parse Error: [12:01:12] -182: dsafsdfFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf^' -182: [12:01:12] [12:01:12] '[12:01:12] -182: SMILESSMILES Parse Error: SMILES Parse Error: -182: Failed parsing SMILES 'dsafsdf' for input: 'Failed parsing SMILES 'dsafsdf'dsafsdf for input: ''dsafsdf Parse Error: ' -182: -182: [12:01:12] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: while parsing: dsafsdf -182: [12:01:12] [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: ' for input: 'dsafsdf' -182: dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: : -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] [12:01:12] [12:01:12] SMILES Parse Error: syntax error[12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[12:01:12] SMILES Parse Error: syntax error[12:01:12] [12:01:12] [12:01:12] [12:01:12] SMILES Parse Error: [12:01:12] [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] [12:01:12] [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1:[12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: while parsing: dsafsdf -182: [12:01:12] [12:01:12] SMILES Parse Error: check for mistakes around position [12:01:12] SMILES Parse Error: SMILES Parse Error: syntax error[12:01:12] SMILES Parse Error: while parsing: SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: syntax errordsafsdf while parsing: dsafsdf -182: -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] ^SMILES Parse Error: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] syntax errordsafsdf -182: [12:01:12] dsafsdfsyntax error -182: while parsing: while parsing: dsafsdf[12:01:12] -182: -182: [12:01:12] ^ -182: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position 1:1: -182: -182: [12:01:12] [12:01:12] SMILES[12:01:12] dsafsdf -182: [12:01:12] ^ -182: ^ -182: dsafsdf -182: [12:01:12] [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: ^ -182: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] [12:01:12] SMILES[12:01:12] [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] [12:01:12] [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: SMILES Parse Error: [12:01:12] -182: SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: SMILES Parse Error: 1syntax error while parsing: dsafsdf -182: : -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: while parsing: dsafsdf -182: [12:01:12] [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: SMILES Parse Error: check for mistakes around position syntax error1[12:01:12] : -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: SMILES Parse Error: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: SMILES Parse Error: syntax errorsyntax error while parsing: dsafsdfSMILES Parse Error: while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: -182: 1[12:01:12] : -182: SMILES Parse Error: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfsyntax error while parsing: dsafsdf -182: [12:01:12] [12:01:12] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position 1:[12:01:12] dsafsdf -182: [12:01:12] ^syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] SMILES Parse Error: [12:01:12] SMILES Parse Error: -182: syntax error while parsing: dsafsdf -182: 'dsafsdf1 -182: SMILES Parse Error: SMILES Parse Error: -182: syntax error[12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: syntax errorsyntax error while parsing: syntax error while parsing: while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1[12:01:12] [12:01:12] dsafsdf: -182: [12:01:12] -182: ^ -182: [12:01:12] dsafsdf -182: [12:01:12] ^: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: -182: dsafsdf -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[12:01:12] [12:01:12] ^[12:01:12] while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: SMILES for input: 'dsafsdf' -182: [12:01:12] Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: -182: dsafsdfSMILES Parse Error: Failed parsing SMILES 'dsafsdf' -182: for input: '[12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[12:01:12] ^ -182: dsafsdf' -182: [12:01:12] SMILES Parse Error: for input: 'dsafsdfFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: ' -182: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] SMILES Parse Error: dsafsdf -182: [12:01:12] ^ -182: ^ -182: SMILES Parse Error: syntax error[12:01:12] [12:01:12] SMILES Parse Error: SMILES Parse Error: check for mistakes around position [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: syntax error while parsing: dsafsdf -182: 1 while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: : -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: dsafsdf -182: [12:01:12] Failed parsing SMILES 'dsafsdf'SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: -182: for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [12:01:12] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [12:01:12] SMILES Parse Error: check for mistakes around position 1: -182: [12:01:12] dsafsdf -182: [12:01:12] ^ -182: [12:01:12] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -75: [12:01:12] Finished: testSmiCorrectness() -75: [12:01:12] ----------------------------------------- -75: -75: [12:01:12] -75: ----------------------------------------- -182: [12:01:12] ------------------------------------- -182: [12:01:12] Results do not depend on numThreads -75: [12:01:12] Spurious data before the first property will be ignored -75: [12:01:12] Property will be truncated after the first blank line -75: [12:01:12] Property will be truncated after the first blank line -75: [12:01:12] Property will be truncated after the first blank line -209/235 Test #206: molTautomerTest ........................ Passed 9.50 sec -210/235 Test #185: testRGroupDecomp ....................... Passed 12.38 sec -75: [12:01:12] Finished: testSDCorrectness() -75: [12:01:12] ----------------------------------------- -75: -211/235 Test #75: testMultithreadedMolSupplier ........... Passed 17.93 sec -211: ............[12:01:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -211: [12:01:14] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -211: [12:01:14] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -211: ........[12:01:14] Explicit valence for atom # 1 O, 3, is greater than permitted -211: .. -211: ---------------------------------------------------------------------- -211: Ran 38 tests in 11.179s -211: -211: OK -211: done -159: Done -159: ----------------- Test Github #781: Rendering single-atom molecules -159: Done -159: ----------------- Test 3 -212/235 Test #211: pyMolStandardize ....................... Passed 12.30 sec -159: file test3_1.png gave hash 4245589364U not the expected 675908852U -159: file test3_2.png gave hash 3367333300U not the expected 2452584093U -159: file test3_3.png gave hash 2996581333U not the expected 1907006999U -159: file test3_4.png gave hash 3977004105U not the expected 2305641511U -159: file test3_5.png gave hash 3967750587U not the expected 3842605920U -159: file test3_6.png gave hash 691593501U not the expected 662622011U -159: file test3_7.png gave hash 1614455692U not the expected 469729412U -159: Done -159: ----------------- Test Github774: upside-down drawings -159: file test774_1.png gave hash 383494043U not the expected 428322245U -159: file test774_2.png gave hash 2504225659U not the expected 4095288521U -159: Done -159: ----------------- Test 9 (molecule legends) -159: file test9_1.svg gave hash 923579170U not the expected 1484349178U -159: Done -159: ----------------- Test Github852: Lines used to wedge bonds are too thick -159: file test852_1.png gave hash 2064209894U not the expected 271517011U -159: file test852_2.png gave hash 869339719U not the expected 967452082U -159: ---------------- -159: ---------------- -159: ---------------- -159: ---------------- -159: Done -159: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right -159: file test860_1.png gave hash 1884717540U not the expected 2835587240U -159: file test860_2.png gave hash 3946798084U not the expected 1116015475U -159: file test860_3.png gave hash 2321130724U not the expected 1872467868U -159: Done -159: ----------------- Test Github #910: ugly coordinates generated for peptide chains -159: Done -159: ----------------- Test Github #932: mistake in SVG for wedged bonds -159: Done -159: ----------------- Test Github #953: default color should not be cyan -159: Done -159: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly -159: Done -159: ----------------- Test Deuterium, Tritium -159: Done -159: ----------------- Test crossed bonds -159: Done -159: ----------------- Testing drawing a second molecule -159: Done -159: ----------------- Testing drawing a grid of molecules -159: Done -159: ----------------- Testing drawMolecules -159: file test12_1.svg gave hash 76786371U not the expected 826649652U -159: Done -159: ----------------- Test JSON Configuration -159: Done -159: ----------------- Testing github 1090: escape html characters in SVG output -159: Done -159: ----------------- Testing github 1035: overflow bug in SVG color generation -159: Done -159: ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes -159: Done -159: ----------------- Testing github 1322: add custom atom labels -159: Done -159: ----------------- Testing use of a black & white palette -159: Done -159: ----------------- Testing use of continuous highlighting with drawMolecules -159: Done -159: ----------------- Test 17 - Testing maximum font size -159: Done -159: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list -159: Done -159: ----------------- Testing use of fixed scales for drawing. -159: Done -159: ----------------- Testing rotation of 2D drawing. -159: Done -159: ----------------- Testing inclusion of molecule metadata -159: Done -159: ----------------- Testing Github2063: Drawing racemic bond stereo as crossed bonds should be the default -159: Done -159: ----------------- Testing Github2151: MolDraw2D: line width should be controlled by MolDrawOptions -159: file testGithub2151_1.svg gave hash 3620378781U not the expected 4119581143U -159: file testGithub2151_2.svg gave hash 3896781930U not the expected 425960913U -159: Done -159: ----------------- Testing testGithub2762: MolDraw2D: HCl and ethane should be drawn -159: Done -159: ----------------- Testing testGithub2931: multi-coloured molecule highlights. -159: file testGithub2931_1.svg gave hash 811930351U not the expected 3635831631U -159: file testGithub2931_3.svg gave hash 1986517899U not the expected 2885834646U -159: Done -159: ----------------- Testing annotation of 2D Drawing. -159: file test20_1.png gave hash 1526801019U not the expected 200877868U -159: file test20_2.png gave hash 1568015929U not the expected 1651164846U -159: file test20_3.png gave hash 2265759724U not the expected 1463603076U -159: file test20_4.png gave hash 960727959U not the expected 1714613205U -159: Done -159: ----------------- Test 21 - different font -159: Done -159: ----------------- Test 22 - draw explicit methyls. -159: Done -159: ----------------- Testing drawing of legends. -159: Done -159: ----------------- Test Github 3305 - change and scale line widths. -159: file testGithub3305_1.png gave hash 4250074512U not the expected 3303791649U -159: file testGithub3305_2.png gave hash 2438913291U not the expected 4003267433U -159: file testGithub3305_3.png gave hash 1680056767U not the expected 273338209U -159: file testGithub3305_4.png gave hash 3967750587U not the expected 3842605920U -159: file testGithub3305_5.png gave hash 2464937348U not the expected 151279576U -159: file testGithub3305_5.svg gave hash 3310590632U not the expected 1335449325U -159: file testGithub3305_6.png gave hash 1984494277U not the expected 613418460U -159: file testGithub3305_7.png gave hash 2361405774U not the expected 2835747678U -159: Done -159: ----------------- Test Github 3391 - maxFontSize interacting badly with DrawMolecules. -159: Done -159: ----------------- Test Github 4156 - bad scale for radicals in grid -159: Done -159: ----------------- Test JSON atomColourPalette -159: Done -159: ----------------- Test draw aromatic OR queries -159: Done -159: ----------------- Test AND queries -159: Done -213/235 Test #159: moldraw2DTest1 ......................... Passed 19.18 sec -214/235 Test #198: pyTestThreads .......................... Passed 15.17 sec -95: 0,0 0 -95: 0,1 0 -95: 1,0 0 -95: 1,1 0 -95: 2,0 0 -95: 2,1 0 -215/235 Test #95: testEnumeration ........................ Passed 23.56 sec -182: [12:01:18] ------------------------------------- -182: [12:01:18] Results do not depend on numThreads (all same) -182: [12:01:18] ------------------------------------- -182: [12:01:18] testTautomerQueries -182: [12:01:18] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -182: [12:01:18] ------------------------------------- -182: [12:01:18] github3881 recursive smarts with rings -216/235 Test #182: substructLibraryTest ................... Passed 20.27 sec -194: ..[12:01:19] +81: =============================================================================== +81: All tests passed (1601 assertions in 100 test cases) +81: +195/235 Test #81: fileParsersCatchTest ................... Passed 78.84 sec +test 215 + Start 215: testMolEnumerator + +215: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator +215: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator +215: Test timeout computed to be: 1500 +196/235 Test #212: testScaffoldNetwork .................... Passed 4.78 sec +test 216 + Start 216: pyMolEnumerator + +216: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" +216: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap +216: Test timeout computed to be: 1500 +215: Randomness seeded to: 1714402604 +215: [09:21:45] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +211: ..........[09:21:45] Explicit valence for atom # 1 N, 4, is greater than permitted +211: [09:21:45] Explicit valence for atom # 1 N, 4, is greater than permitted +215: =============================================================================== +215: All tests passed (321 assertions in 16 test cases) +215: +211: [09:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197/235 Test #215: testMolEnumerator ...................... Passed 0.27 sec +test 217 + Start 217: testAbbreviations + +217: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations +217: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations +217: Test timeout computed to be: 1500 +211: [09:21:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +194: ..[09:21:45] 194: 194: **** +217: Randomness seeded to: 3191174530 +217: [09:21:45] SMARTS Parse Error: syntax error while parsing: *fail +217: [09:21:45] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' 194: Pre-condition Violation 194: no owner 194: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h @@ -33931,7 +33951,7 @@ 194: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x00007FC6DC9CB66C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x00007F6BBAF2066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -33942,17 +33962,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x00007FC6DA3B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x00007FC6DA3B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x00007FC6DA3B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x00007FC6DA3B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x00007FC6DA3B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x00007F6BB85B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x00007F6BB85B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x00007F6BB85B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x00007F6BB85B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x00007F6BB85B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x00007FC6DC9C8406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x00007F6BBAF1D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005BEE79 in /usr/bin/python3 @@ -33984,15 +34004,20 @@ 194: 55# 0x000000000067EB1E in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x00007FC6DD3B3D68 in /lib/x86_64-linux-gnu/libc.so.6 +194: 58# 0x00007F6BBB73ED68 in /lib/x86_64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: [12:01:19] +194: [09:21:45] 194: 194: **** +217: [09:21:45] no suitable SubstanceGroups found +217: =============================================================================== +217: All tests passed (195 assertions in 12 test cases) +217: +198/235 Test #217: testAbbreviations ...................... Passed 0.11 sec 194: Pre-condition Violation 194: no owner 194: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h @@ -34004,7 +34029,7 @@ 194: 2# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x00007FC6DC9CB66C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x00007F6BBAF2066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34015,17 +34040,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x00007FC6DA3B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x00007FC6DA3B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x00007FC6DA3B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x00007FC6DA3B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x00007FC6DA3B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x00007F6BB85B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x00007F6BB85B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x00007F6BB85B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x00007F6BB85B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x00007F6BB85B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x00007FC6DC9C8406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x00007F6BBAF1D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005BEE79 in /usr/bin/python3 @@ -34057,13 +34082,13 @@ 194: 55# 0x000000000067EB1E in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x00007FC6DD3B3D68 in /lib/x86_64-linux-gnu/libc.so.6 +194: 58# 0x00007F6BBB73ED68 in /lib/x86_64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: [12:01:19] +194: [09:21:45] 194: 194: **** 194: Pre-condition Violation @@ -34077,7 +34102,7 @@ 194: 2# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x00007FC6DC9CB66C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x00007F6BBAF2066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34088,17 +34113,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x00007FC6DA3B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x00007FC6DA3B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x00007FC6DA3B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x00007FC6DA3B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x00007FC6DA3B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x00007F6BB85B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x00007F6BB85B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x00007F6BB85B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x00007F6BB85B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x00007F6BB85B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x00007FC6DC9C8406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x00007F6BBAF1D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005BEE79 in /usr/bin/python3 @@ -34130,13 +34155,13 @@ 194: 55# 0x000000000067EB1E in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x00007FC6DD3B3D68 in /lib/x86_64-linux-gnu/libc.so.6 +194: 58# 0x00007F6BBB73ED68 in /lib/x86_64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: [12:01:19] +194: [09:21:45] 194: 194: **** 194: Pre-condition Violation @@ -34150,7 +34175,7 @@ 194: 2# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x00007FC6DC9CB66C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x00007F6BBAF2066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34161,17 +34186,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x00007FC6DA3B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x00007FC6DA3B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x00007FC6DA3B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x00007FC6DA3B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x00007FC6DA3B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x00007F6BB85B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x00007F6BB85B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x00007F6BB85B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x00007F6BB85B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x00007F6BB85B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x00007FC6DC9C8406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x00007F6BBAF1D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005BEE79 in /usr/bin/python3 @@ -34203,15 +34228,21 @@ 194: 55# 0x000000000067EB1E in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x00007FC6DD3B3D68 in /lib/x86_64-linux-gnu/libc.so.6 +194: 58# 0x00007F6BBB73ED68 in /lib/x86_64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: [12:01:19] +194: [09:21:45] 194: 194: **** +test 218 + Start 218: pyAbbreviations + +218: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" +218: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap +218: Test timeout computed to be: 1500 194: Pre-condition Violation 194: no owner 194: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h @@ -34223,7 +34254,7 @@ 194: 2# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x00007FC6DC9CB66C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x00007F6BBAF2066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34234,17 +34265,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x00007FC6DA3B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x00007FC6DA3B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x00007FC6DA3B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x00007FC6DA3B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x00007FC6DA3B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x00007F6BB85B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x00007F6BB85B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x00007F6BB85B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x00007F6BB85B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x00007F6BB85B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x00007FC6DC9C8406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x00007F6BBAF1D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005BEE79 in /usr/bin/python3 @@ -34276,13 +34307,13 @@ 194: 55# 0x000000000067EB1E in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x00007FC6DD3B3D68 in /lib/x86_64-linux-gnu/libc.so.6 +194: 58# 0x00007F6BBB73ED68 in /lib/x86_64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: .....[12:01:19] +194: .....[09:21:45] 194: 194: **** 194: Range Error @@ -34296,7 +34327,7 @@ 194: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x00007FC6DC9CB66C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x00007F6BBAF2066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34307,17 +34338,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x00007FC6DA3B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x00007FC6DA3B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x00007FC6DA3B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x00007FC6DA3B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x00007FC6DA3B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x00007F6BB85B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x00007F6BB85B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x00007F6BB85B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x00007F6BB85B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x00007F6BB85B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x00007FC6DC9C8406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x00007F6BBAF1D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005BEE79 in /usr/bin/python3 @@ -34349,51 +34380,56 @@ 194: 55# 0x000000000067EB1E in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x00007FC6DD3B3D68 in /lib/x86_64-linux-gnu/libc.so.6 +194: 58# 0x00007F6BBB73ED68 in /lib/x86_64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: ......[12:01:19] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -194: [12:01:19] ERROR: Smiles parse error on line 0 -194: [12:01:19] ERROR: Cannot create molecule from : 'c1ccccc' -194: [12:01:19] SMILES Parse Error: extra open parentheses while parsing: C(C -194: [12:01:19] SMILES Parse Error: check for mistakes around position 2: -194: [12:01:19] C(C -194: [12:01:19] ~^ -194: [12:01:19] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -194: [12:01:19] ERROR: Smiles parse error on line 3 -194: [12:01:19] ERROR: Cannot create molecule from : 'C(C' -194: [12:01:19] Explicit valence for atom # 1 C, 5, is greater than permitted -194: [12:01:19] ERROR: Could not sanitize molecule on line 6 -194: [12:01:19] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -194: [12:01:19] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -194: [12:01:19] ERROR: Smiles parse error on line 0 -194: [12:01:19] ERROR: Cannot create molecule from : 'c1ccccc' -194: [12:01:19] SMILES Parse Error: extra open parentheses while parsing: C(C -194: [12:01:19] SMILES Parse Error: check for mistakes around position 2: -194: [12:01:19] C(C -194: [12:01:19] ~^ -194: [12:01:19] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -194: [12:01:19] ERROR: Smiles parse error on line 3 -194: [12:01:19] ERROR: Cannot create molecule from : 'C(C' -194: [12:01:19] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -194: [12:01:19] ERROR: Smiles parse error on line 6 -194: [12:01:19] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -194: [12:01:19] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [12:01:19] ERROR: Could not sanitize molecule ending on line 21 -194: [12:01:19] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -194: [12:01:19] ERROR: EOF hit while reading atoms -194: [12:01:19] ERROR: moving to the beginning of the next molecule -194: [12:01:19] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [12:01:19] ERROR: Could not sanitize molecule ending on line 21 -194: [12:01:19] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -194: [12:01:19] ERROR: EOF hit while reading atoms -194: [12:01:19] ERROR: moving to the beginning of the next molecule -194: ....[12:01:19] +194: ......[09:21:45] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +194: [09:21:45] ERROR: Smiles parse error on line 0 +194: [09:21:45] ERROR: Cannot create molecule from : 'c1ccccc' +194: [09:21:45] SMILES Parse Error: extra open parentheses while parsing: C(C +194: [09:21:45] SMILES Parse Error: check for mistakes around position 2: +194: [09:21:45] C(C +194: [09:21:45] ~^ +194: [09:21:45] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +194: [09:21:45] ERROR: Smiles parse error on line 3 +194: [09:21:45] ERROR: Cannot create molecule from : 'C(C' +194: [09:21:45] Explicit valence for atom # 1 C, 5, is greater than permitted +194: [09:21:45] ERROR: Could not sanitize molecule on line 6 +194: [09:21:45] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +194: [09:21:45] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +194: [09:21:45] ERROR: Smiles parse error on line 0 +194: [09:21:45] ERROR: Cannot create molecule from : 'c1ccccc' +194: [09:21:45] SMILES Parse Error: extra open parentheses while parsing: C(C +194: [09:21:45] SMILES Parse Error: check for mistakes around position 2: +194: [09:21:45] C(C +194: [09:21:45] ~^ +194: [09:21:45] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +194: [09:21:45] ERROR: Smiles parse error on line 3 +194: [09:21:45] ERROR: Cannot create molecule from : 'C(C' +194: [09:21:45] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +194: [09:21:45] ERROR: Smiles parse error on line 6 +194: [09:21:45] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +194: [09:21:45] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [09:21:45] ERROR: Could not sanitize molecule ending on line 21 +194: [09:21:45] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +194: [09:21:45] ERROR: EOF hit while reading atoms +194: [09:21:45] ERROR: moving to the beginning of the next molecule +194: [09:21:45] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [09:21:45] ERROR: Could not sanitize molecule ending on line 21 +194: [09:21:45] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +194: [09:21:45] ERROR: EOF hit while reading atoms +194: [09:21:45] ERROR: moving to the beginning of the next molecule +194: ....[09:21:45] 194: 194: **** +214: . +214: ---------------------------------------------------------------------- +214: Ran 1 test in 0.063s +214: +214: OK 194: Pre-condition Violation 194: RingInfo not initialized 194: Violation occurred on line 170 in file ./Code/GraphMol/RingInfo.cpp @@ -34405,7 +34441,7 @@ 194: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x00007FC6DC9CB66C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x00007F6BBAF2066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34416,17 +34452,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x00007FC6DA3B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x00007FC6DA3B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x00007FC6DA3B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x00007FC6DA3B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x00007FC6DA3B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x00007F6BB85B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x00007F6BB85B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x00007F6BB85B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x00007F6BB85B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x00007F6BB85B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x00007FC6DC9C8406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x00007F6BBAF1D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005BEE79 in /usr/bin/python3 @@ -34458,13 +34494,21 @@ 194: 55# 0x000000000067EB1E in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x00007FC6DD3B3D68 in /lib/x86_64-linux-gnu/libc.so.6 +194: 58# 0x00007F6BBB73ED68 in /lib/x86_64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: .............[12:01:19] +29: done +199/235 Test #29: testMMFFForceField ..................... Passed 81.55 sec +test 219 + Start 219: generalizedSubstructCatch + +219: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch +219: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct +219: Test timeout computed to be: 1500 +194: .............[09:21:46] 194: 194: **** 194: Range Error @@ -34478,7 +34522,7 @@ 194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x00007FC6DC9CB66C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x00007F6BBAF2066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34489,17 +34533,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x00007FC6DA3B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x00007FC6DA3B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x00007FC6DA3B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x00007FC6DA3B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x00007FC6DA3B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x00007F6BB85B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x00007F6BB85B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x00007F6BB85B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x00007F6BB85B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x00007F6BB85B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x00007FC6DC9C8406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x00007F6BBAF1D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005BEE79 in /usr/bin/python3 @@ -34531,469 +34575,76 @@ 194: 55# 0x000000000067EB1E in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x00007FC6DD3B3D68 in /lib/x86_64-linux-gnu/libc.so.6 +194: 58# 0x00007F6BBB73ED68 in /lib/x86_64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: ...[12:01:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -194: ............................[12:01:19] SMILES Parse Error: unclosed ring for input: 'C1CC' +194: ...[09:21:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +200/235 Test #214: pyScaffoldNetworkPickling .............. Passed 1.01 sec +test 220 + Start 220: pyGeneralizedSubstruct + +220: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" +220: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap +220: Test timeout computed to be: 1500 +194: ............................[09:21:46] SMILES Parse Error: unclosed ring for input: 'C1CC' 194: ......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| -194: 294 -194: ..[12:01:19] WARNING: not removing hydrogen atom without neighbors -194: [12:01:19] WARNING: not removing hydrogen atom with dummy atom neighbors -194: [12:01:19] WARNING: not removing hydrogen atom with wedged bond -194: [12:01:19] WARNING: not removing hydrogen atom without neighbors -194: [12:01:19] WARNING: not removing hydrogen atom with dummy atom neighbors -29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -194: ......[12:01:19] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [12:01:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 -194: .[12:01:19] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [12:01:19] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [12:01:19] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [12:01:19] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [12:01:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 -194: [12:01:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 -194: [12:01:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 -194: ..........[12:01:20] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -194: [12:01:20] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -194: .[12:01:20] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -194: [12:01:20] SMILES Parse Error: check for mistakes around position 4: -194: [12:01:20] CCC |$foo;;bar$| ourname -194: [12:01:20] ~~~^ -194: [12:01:20] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -194: ..[12:01:20] SMILES Parse Error: syntax error while parsing: error -194: [12:01:20] SMILES Parse Error: check for mistakes around position 1: -194: [12:01:20] error -194: [12:01:20] ^ -194: [12:01:20] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -194: [12:01:20] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -194: [12:01:20] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -194: [12:01:20] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -194: .........................[12:01:20] SMILES Parse Error: syntax error while parsing: garbage_0 -194: [12:01:20] SMILES Parse Error: check for mistakes around position 1: -194: [12:01:20] garbage_0 -194: [12:01:20] ^ -194: [12:01:20] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -194: [12:01:20] SMILES Parse Error: syntax error while parsing: garbage_2 -194: [12:01:20] SMILES Parse Error: check for mistakes around position 1: -194: [12:01:20] garbage_2 -194: [12:01:20] ^ -194: [12:01:20] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -194: [12:01:20] SMILES Parse Error: syntax error while parsing: garbage_4 -194: [12:01:20] SMILES Parse Error: check for mistakes around position 1: -194: [12:01:20] garbage_4 -194: [12:01:20] ^ -194: [12:01:20] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' -194: ............ -194: ---------------------------------------------------------------------- -194: Ran 279 tests in 17.602s -194: -194: OK -194: supplier: -194: supplier: -194: supplier: -217/235 Test #194: pyGraphMolWrap ......................... Passed 19.25 sec -29: All 191 tests passed -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -176: VS001: PASSED -176: VS002: PASSED -176: VS003: PASSED -176: VS004: PASSED -176: VS005: PASSED -176: VS006: PASSED -176: VS007: PASSED -176: VS008: PASSED -176: VS009: PASSED -176: VS010: PASSED -176: VS011: PASSED -176: VS012: PASSED -176: VS013: PASSED -176: VS014: PASSED -176: VS015: PASSED -176: VS016: PASSED -176: VS017: PASSED -176: VS018: PASSED -176: VS019: PASSED -176: VS020: PASSED -176: VS021: PASSED -176: VS022: PASSED -176: VS023: PASSED -176: VS024: PASSED -176: VS025: PASSED -176: VS026: PASSED -176: VS027: PASSED -176: VS028: PASSED -176: VS029: PASSED -176: VS030: PASSED -176: VS031: PASSED -176: VS032: PASSED -176: VS033: PASSED -176: VS034: PASSED -176: VS035: PASSED -176: VS036: PASSED -176: VS037: PASSED -176: VS038: PASSED -176: VS039: PASSED -176: VS040: PASSED -176: VS041: PASSED -176: VS042: PASSED -176: VS043: PASSED -176: VS044: PASSED -176: VS045: PASSED -176: VS046: PASSED -176: VS047: PASSED -176: VS048: PASSED -176: VS049: PASSED -176: VS050: PASSED -176: VS051: PASSED -176: VS052: PASSED -176: VS053: PASSED -176: VS054: PASSED -176: VS055: PASSED -176: VS056: PASSED -176: VS057: PASSED -176: VS058: PASSED -176: VS059: PASSED -176: VS060: PASSED -176: VS061: PASSED -176: VS062: PASSED -176: VS063: PASSED -176: VS064: PASSED -176: VS065: PASSED -176: VS066: PASSED -176: VS067: PASSED -176: VS068: PASSED -176: VS069: PASSED -176: VS070: PASSED -176: VS071: PASSED -176: VS072: PASSED -176: VS073: PASSED -176: VS074: PASSED -176: VS075: PASSED -176: VS076: PASSED -176: VS077: PASSED -176: VS078: PASSED -176: VS079: PASSED -176: VS080: PASSED -176: VS081: PASSED -176: VS082: PASSED -176: VS083: PASSED -176: VS084: PASSED -176: VS085: PASSED -176: VS086: PASSED -176: VS087: PASSED -176: VS088: PASSED -176: VS089: PASSED -176: VS090: PASSED -176: VS091: PASSED -176: VS092: PASSED -176: VS093: PASSED -176: VS094: PASSED -176: VS095: PASSED -176: VS096: PASSED -176: VS097: PASSED -176: VS098: PASSED -176: VS099: PASSED -176: VS100: PASSED -176: VS101: PASSED -176: VS102: PASSED -176: VS103: PASSED -176: VS104: PASSED -176: VS105: PASSED -176: VS106: PASSED -176: VS107: PASSED -176: VS108: PASSED -176: VS109: PASSED -176: VS110: PASSED -176: VS111: PASSED -176: VS112: PASSED -176: VS113: PASSED -176: VS114: PASSED -176: VS115: PASSED -176: VS116: PASSED -176: VS117: PASSED -176: VS118: PASSED -176: VS119: PASSED -176: VS120: PASSED -176: VS121: PASSED -176: VS122: PASSED -176: VS123: PASSED -176: VS124: PASSED -176: VS125: PASSED -176: VS126: PASSED -176: VS127: PASSED -176: VS128: PASSED -176: VS129: PASSED -176: VS130: PASSED -176: VS131: PASSED -176: VS132: PASSED -176: VS133: PASSED -176: VS134: PASSED -176: VS135: PASSED -176: VS136: PASSED -176: VS137: PASSED -176: VS138: PASSED -176: VS139: PASSED -176: VS140: PASSED -176: VS141: PASSED -176: VS142: PASSED -176: VS143: PASSED -176: VS144: PASSED -176: VS145: PASSED -176: VS146: PASSED -176: VS147: PASSED -176: VS148: PASSED -176: VS149: PASSED -176: VS150: PASSED -176: VS151: PASSED -176: VS152: PASSED -176: VS153: PASSED -176: VS154: PASSED -176: VS155: PASSED -176: VS156: PASSED -176: VS157: PASSED -176: VS158: PASSED -176: VS159: PASSED -176: VS160: PASSED -176: VS161: PASSED -176: VS162: PASSED -176: VS163: PASSED -176: VS164: PASSED -176: VS165: PASSED -176: VS166: PASSED -176: VS167: PASSED -176: VS168: PASSED -176: VS169: PASSED -176: VS170: PASSED -176: VS171: PASSED -176: VS172: PASSED -176: VS173: PASSED -176: VS174: PASSED -176: VS175: PASSED -176: VS176: PASSED -176: VS177: PASSED -176: VS178: PASSED -176: VS179: PASSED -176: VS180: PASSED -176: VS181: PASSED -176: VS182: PASSED -176: VS183: PASSED -176: VS184: PASSED -176: VS185: PASSED -176: VS186: PASSED -176: VS187: PASSED -176: VS188: PASSED -176: VS189: PASSED -176: VS190: PASSED -176: VS191: PASSED -176: VS192: PASSED -176: VS193: PASSED -176: VS194: PASSED -176: VS195: PASSED -176: VS196: PASSED -176: VS197: PASSED -176: VS198: PASSED -176: VS199: PASSED -176: VS200: PASSED -176: VS201: PASSED -176: VS202: PASSED -176: VS203: PASSED -176: VS204: PASSED -176: VS205: PASSED -176: VS206: PASSED -176: VS207: PASSED -176: VS208: PASSED -176: VS209: PASSED -176: VS210: PASSED -176: VS211: PASSED -176: VS212: PASSED -176: VS213: PASSED -176: VS214: PASSED -176: VS215: PASSED -176: VS216: PASSED -176: VS217: PASSED -176: VS218: PASSED -176: VS219: PASSED -176: VS220: PASSED -176: VS221: PASSED -176: VS222: PASSED -176: VS223: PASSED -176: VS224: PASSED -176: VS225: PASSED -176: VS226: PASSED -176: VS227: PASSED -176: VS228: PASSED -176: VS229: PASSED -176: VS230: PASSED -176: VS231: PASSED -176: VS232: PASSED -176: VS233: PASSED -176: VS234: PASSED -176: VS235: PASSED -176: VS236: PASSED -176: VS237: PASSED -176: VS238: PASSED -176: VS239: PASSED -176: VS240: PASSED -176: VS241: PASSED -176: VS242: PASSED -176: VS243: PASSED -176: VS244: PASSED -176: VS245: PASSED -176: VS246: PASSED -176: VS247: PASSED -176: VS248: PASSED -176: VS249: PASSED -176: VS250: PASSED -176: VS251: PASSED -176: VS252: PASSED -176: VS253: PASSED -176: VS254: PASSED -176: VS255: PASSED -176: VS256: PASSED -176: VS257: PASSED -176: VS258: PASSED -176: VS259: PASSED -176: VS260: PASSED -176: VS261: PASSED -176: VS262: PASSED -176: VS263: PASSED -176: VS264: PASSED -176: VS265: PASSED -176: VS266: PASSED -176: VS267: PASSED -176: VS268: PASSED -176: VS269: PASSED -176: VS270: PASSED -176: VS271: PASSED -176: VS272: PASSED -176: VS273: PASSED -176: VS274: PASSED -176: VS275: PASSED -176: VS276: PASSED -176: VS277: PASSED -176: VS278: PASSED -176: VS279: PASSED -176: VS280: PASSED -176: VS281: PASSED -176: VS282: PASSED -176: VS283: PASSED -176: VS284: PASSED -176: VS285: PASSED -176: VS286: PASSED -176: VS287: PASSED -176: VS288: PASSED -176: VS289: PASSED -176: VS290: PASSED -176: VS291: PASSED -176: VS292: PASSED -176: VS293: PASSED -176: VS294: PASSED -176: VS295: PASSED -176: VS296: PASSED -176: VS297: PASSED -176: VS298: PASSED -176: VS299: PASSED -176: VS300: PASSED -176: Check finished: 0 molecules failed. -176: Failed: -81: =============================================================================== -81: All tests passed (1601 assertions in 100 test cases) -81: -218/235 Test #81: fileParsersCatchTest ................... Passed 25.35 sec -219/235 Test #176: pyCIPLabelsValidation .................. Passed 22.22 sec -152: .............[12:01:20] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:01:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:01:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:01:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:01:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:01:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:01:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:01:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:01:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:01:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:01:21] Molecule does not have explicit Hs. Consider calling AddHs() -152: ...[12:01:25] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:01:25] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:01:25] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:01:25] Molecule does not have explicit Hs. Consider calling AddHs() -152: [12:01:25] Molecule does not have explicit Hs. Consider calling AddHs() -52: Randomness seeded to: 1939954469 -52: =============================================================================== -52: All tests passed (14835 assertions in 14 test cases) -52: -220/235 Test #52: canonTestsCatch ........................ Passed 30.61 sec -152: ... -152: ---------------------------------------------------------------------- -152: Ran 19 tests in 27.797s -152: -152: OK -152: Testing MolAlign Wrappers -221/235 Test #152: pyMolAlign ............................. Passed 28.62 sec -173: Query 0 -29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -29: All 191 tests passed -29: done -29: ------------------------------------- -29: Unit tests for all MMFF constraint terms. -29: 10.0003 -29: done -29: ------------------------------------- -29: Unit test for MMFF TorsionConstraint close to 0 degrees. -29: done -29: ------------------------------------- -29: Unit tests for copying MMFF ForceFields. -29: done -29: ------------------------------------- -29: Unit test for MMFF butane scan. -29: done -222/235 Test #29: testMMFFForceField ..................... Passed 33.63 sec -148: .........[12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -148: [12:01:31] Molecule does not have explicit Hs. Consider calling AddHs() -173: Query 1 -150: --------------------------------- -150: test O3A multithreading bug -150: -150: --------------------------------- -150: testCrippenO3A multithreading -150: -150: generating reference data -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 38.14 seconds -223/235 Test #163: testFMCS ............................... Passed 38.72 sec -150: processing -150: launch :0 -150: launch :1 -150: launch :2 -150: launch :3 -184: ......[12:01:37] +194: 1 +194: ..[09:21:46] WARNING: not removing hydrogen atom without neighbors +194: [09:21:46] WARNING: not removing hydrogen atom with dummy atom neighbors +194: [09:21:46] WARNING: not removing hydrogen atom with wedged bond +194: [09:21:46] WARNING: not removing hydrogen atom without neighbors +194: [09:21:46] WARNING: not removing hydrogen atom with dummy atom neighbors +216: ... +216: ---------------------------------------------------------------------- +216: Ran 3 tests in 0.054s +216: +216: OK +218: ....... +218: ---------------------------------------------------------------------- +218: Ran 7 tests in 0.086s +218: +218: OK +220: ....... +220: ---------------------------------------------------------------------- +220: Ran 7 tests in 0.253s +220: +220: OK +201/235 Test #220: pyGeneralizedSubstruct ................. Passed 0.87 sec +test 221 + Start 221: testMolProcessing + +221: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing +221: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing +221: Test timeout computed to be: 1500 +219: Randomness seeded to: 2751037758 +219: =============================================================================== +219: All tests passed (486 assertions in 10 test cases) +219: +202/235 Test #219: generalizedSubstructCatch .............. Passed 1.22 sec +test 222 + Start 222: pyMolProcessing + +222: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" +222: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap +222: Test timeout computed to be: 1500 +203/235 Test #218: pyAbbreviations ........................ Passed 1.44 sec +test 223 + Start 223: testMIF + +223: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF +223: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields +223: Test timeout computed to be: 1500 +204/235 Test #216: pyMolEnumerator ........................ Passed 1.87 sec +test 224 + Start 224: pyMIF + +224: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" +224: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap +224: Test timeout computed to be: 1500 +184: ......[09:21:47] 184: 184: **** 184: Pre-condition Violation @@ -35014,25 +34665,25 @@ 184: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 184: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 184: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -184: 12# 0x00007F42B525A4F5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +184: 12# 0x00007F0F3165A4F5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 184: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -184: 14# 0x00007F42B767A66C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +184: 14# 0x00007F0F33A6066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 184: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 184: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 184: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 184: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 184: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -184: 20# 0x00007F42B51B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -184: 21# 0x00007F42B51B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -184: 22# 0x00007F42B51B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -184: 23# 0x00007F42B51B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -184: 24# 0x00007F42B51B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +184: 20# 0x00007F0F315B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +184: 21# 0x00007F0F315B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +184: 22# 0x00007F0F315B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +184: 23# 0x00007F0F315B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +184: 24# 0x00007F0F315B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 184: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 184: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 184: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 184: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 184: 29# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -184: 30# 0x00007F42B7677406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +184: 30# 0x00007F0F33A5D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 184: 31# _PyObject_MakeTpCall in /usr/bin/python3 184: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 33# 0x00000000005BEE79 in /usr/bin/python3 @@ -35064,13 +34715,13 @@ 184: 59# 0x000000000067EB1E in /usr/bin/python3 184: 60# Py_RunMain in /usr/bin/python3 184: 61# Py_BytesMain in /usr/bin/python3 -184: 62# 0x00007F42B7FBCD68 in /lib/x86_64-linux-gnu/libc.so.6 +184: 62# 0x00007F0F343B6D68 in /lib/x86_64-linux-gnu/libc.so.6 184: 63# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 184: 64# _start in /usr/bin/python3 184: ---------- 184: **** 184: -184: [12:01:37] +184: [09:21:47] 184: 184: **** 184: Pre-condition Violation @@ -35082,7 +34733,7 @@ 184: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 184: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 184: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -184: 3# 0x00007F42B4CE5E60 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +184: 3# 0x00007F0F310E5E60 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 184: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 184: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 184: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 @@ -35092,25 +34743,25 @@ 184: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 184: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 184: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -184: 13# 0x00007F42B525A4F5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +184: 13# 0x00007F0F3165A4F5 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 184: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -184: 15# 0x00007F42B767A66C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +184: 15# 0x00007F0F33A6066C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 184: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 184: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 184: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 184: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 184: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -184: 21# 0x00007F42B51B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -184: 22# 0x00007F42B51B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -184: 23# 0x00007F42B51B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -184: 24# 0x00007F42B51B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -184: 25# 0x00007F42B51B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +184: 21# 0x00007F0F315B5893 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +184: 22# 0x00007F0F315B5863 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +184: 23# 0x00007F0F315B5833 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +184: 24# 0x00007F0F315B5803 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +184: 25# 0x00007F0F315B57D3 in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 184: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 184: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 184: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 184: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so 184: 30# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -184: 31# 0x00007F42B7677406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +184: 31# 0x00007F0F33A5D406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 184: 32# _PyObject_MakeTpCall in /usr/bin/python3 184: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 184: 34# 0x00000000005BEE79 in /usr/bin/python3 @@ -35142,40 +34793,429 @@ 184: 60# 0x000000000067EB1E in /usr/bin/python3 184: 61# Py_RunMain in /usr/bin/python3 184: 62# Py_BytesMain in /usr/bin/python3 -184: 63# 0x00007F42B7FBCD68 in /lib/x86_64-linux-gnu/libc.so.6 +184: 63# 0x00007F0F343B6D68 in /lib/x86_64-linux-gnu/libc.so.6 184: 64# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 184: 65# _start in /usr/bin/python3 184: ---------- 184: **** 184: -209: [12:01:37] Explicit valence for atom # 0 Br, 1, is greater than permitted +206: CN=c1cc[nH]cn1 +206: CN=c1ccnc[nH]1 +206: CNc1ccncn1 +206: res: CNc1ccncn1 +206: CN=c1cccc[nH]1 +206: CNc1ccccn1 +206: res: CNc1ccccn1 +223: Randomness seeded to: 679537073 +223: =============================================================================== +223: All tests passed (27926 assertions in 8 test cases) +223: +205/235 Test #223: testMIF ................................ Passed 0.39 sec +test 225 + Start 225: testQuery + +225: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Query/testQuery +225: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Query +225: Test timeout computed to be: 1500 +225: Query +225: Query2 +225: Equality +225: Greater +225: GreaterEqual +225: Less +225: LessEqual +225: Open Range +225: Closed Range +225: Float +225: With Tolerance +225: Set +225: And +225: Or +225: XOr +225: pointer and copy foo +225: Set2 +206/235 Test #225: testQuery .............................. Passed 0.03 sec +test 226 + Start 226: testBaseFeatures + +226: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Features/testBaseFeatures +226: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/Features +226: Test timeout computed to be: 1500 +226: ------------------------------------- +226: Basics for ExplicitFeatures. +226: done +226: ------------------------------------- +226: Basics for ImplicitFeatures. +226: done +226: ------------------------------------- +226: ExplicitFeatures 2D, string type. +226: done +207/235 Test #226: testBaseFeatures ....................... Passed 0.03 sec +test 227 + Start 227: testMatCalc + +227: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc +227: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc +227: Test timeout computed to be: 1500 +227: 1.68022e+08 +227: 1.73149e+08 +227: 1.05549e+08 +227: 7.20603e+07 +227: 1.41535e+08 +227: 1.08592e+08 +227: 1.11334e+08 +227: 2.05553e+08 +227: 1.54962e+08 +227: 8.08231e+07 +227: 5.61421e+07 +227: 1.28874e+08 +227: 1.59011e+08 +227: 8.69902e+07 +227: 1.31367e+08 +227: 2.27389e+08 +227: 1.60289e+08 +227: 7.79813e+07 +227: 1.61001e+08 +227: 2.07599e+08 +227: 2.24432e+08 +227: 1.39725e+08 +227: 2.42614e+08 +227: 1.77578e+08 +227: 1.05908e+08 +227: 9.06742e+07 +227: 1.8087e+08 +227: 1.98182e+08 +227: 2.03052e+08 +227: 1.7673e+08 +227: 9.32798e+07 +227: 1.37969e+08 +227: 1.83778e+08 +227: 2.1228e+08 +227: 5.06157e+07 +227: 1.566e+08 +227: 2.37142e+08 +227: 1.49345e+08 +227: 7.05819e+07 +227: 1.71633e+08 +227: 1.96817e+08 +227: 2.18246e+08 +227: 9.49496e+07 +227: 2.25618e+08 +227: 1.30219e+08 +208/235 Test #227: testMatCalc ............................ Passed 0.03 sec +test 228 + Start 228: pyMatCalc + +228: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" +228: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap +228: Test timeout computed to be: 1500 +209/235 Test #206: molTautomerTest ........................ Passed 13.28 sec +test 229 + Start 229: testSimDivPickers + +229: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers/testSimDivPickers +229: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers +229: Test timeout computed to be: 1500 +229: [09:21:47] ------------------------------------- +229: [09:21:47] Testing github issue 1421: MaxMinPicker picking non-existent element. +229: [09:21:47] Done +229: [09:21:47] ------------------------------------- +229: [09:21:47] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +229: [09:21:47] Done +210/235 Test #229: testSimDivPickers ...................... Passed 0.03 sec +test 230 + Start 230: pickersTestsCatch + +230: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers/pickersTestsCatch +230: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers +230: Test timeout computed to be: 1500 +194: ......[09:21:48] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [09:21:48] Can't kekulize mol. Unkekulized atoms: 0 1 2 +194: .[09:21:48] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [09:21:48] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [09:21:48] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [09:21:48] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [09:21:48] Can't kekulize mol. Unkekulized atoms: 0 1 2 +194: [09:21:48] Can't kekulize mol. Unkekulized atoms: 0 1 2 +194: [09:21:48] Can't kekulize mol. Unkekulized atoms: 0 1 2 +230: Randomness seeded to: 419109142 +230: =============================================================================== +230: All tests passed (21267 assertions in 1 test case) +230: +211/235 Test #230: pickersTestsCatch ...................... Passed 0.28 sec +test 231 + Start 231: pySimDivPickers + +231: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/Wrap/testPickers.py" +231: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap +231: Test timeout computed to be: 1500 +194: ..........[09:21:48] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +194: [09:21:48] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +194: .[09:21:48] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +194: [09:21:48] SMILES Parse Error: check for mistakes around position 4: +194: [09:21:48] CCC |$foo;;bar$| ourname +194: [09:21:48] ~~~^ +194: [09:21:48] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +194: ..[09:21:48] SMILES Parse Error: syntax error while parsing: error +194: [09:21:48] SMILES Parse Error: check for mistakes around position 1: +194: [09:21:48] error +194: [09:21:48] ^ +194: [09:21:48] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +194: [09:21:48] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +194: [09:21:48] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +194: [09:21:48] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +194: .........................[09:21:48] SMILES Parse Error: syntax error while parsing: garbage_0 +194: [09:21:48] SMILES Parse Error: check for mistakes around position 1: +194: [09:21:48] garbage_0 +194: [09:21:48] ^ +194: [09:21:48] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +194: [09:21:48] SMILES Parse Error: syntax error while parsing: garbage_2 +194: [09:21:48] SMILES Parse Error: check for mistakes around position 1: +194: [09:21:48] garbage_2 +194: [09:21:48] ^ +194: [09:21:48] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +194: [09:21:48] SMILES Parse Error: syntax error while parsing: garbage_4 +194: [09:21:48] SMILES Parse Error: check for mistakes around position 1: +194: [09:21:48] garbage_4 +194: [09:21:48] ^ +194: [09:21:48] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +194: ............ +194: ---------------------------------------------------------------------- +194: Ran 279 tests in 24.660s +194: +194: OK +194: supplier: +194: supplier: +194: supplier: +224: ....... +224: ---------------------------------------------------------------------- +224: Ran 7 tests in 0.326s +224: +224: OK +224: Testing MIF wrapper +212/235 Test #224: pyMIF .................................. Passed 1.86 sec +test 232 + Start 232: pyRanker + +232: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/Wrap/testRanker.py" +232: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap +232: Test timeout computed to be: 1500 +213/235 Test #194: pyGraphMolWrap ......................... Passed 27.23 sec +231: [09:21:49] the useCache argument is deprecated and ignored +test 233 + Start 233: testChemicalFeatures + +233: Test command: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures +233: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures +233: Test timeout computed to be: 1500 +233: ----------------------------------------- +233: Test1 +233: Done +214/235 Test #233: testChemicalFeatures ................... Passed 0.01 sec +test 234 + Start 234: pyFeatures + +234: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/Wrap/testFeatures.py" +234: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap +234: Test timeout computed to be: 1500 +211: ............[09:21:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +211: [09:21:49] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +211: [09:21:49] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +222: .. +222: ---------------------------------------------------------------------- +222: Ran 2 tests in 1.877s +222: +222: OK +231: ...[09:21:50] the useCache argument is deprecated and ignored +231: [09:21:50] the useCache argument is deprecated and ignored +231: .[09:21:50] the useCache argument is deprecated and ignored +232: ..[09:21:50] +232: +232: **** +232: Invariant Violation +232: Can't rank more bits than the ensemble size +232: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp +232: Failed Expression: num <= dp_maskBits->getNumOnBits() +232: ---------- +232: Stacktrace: +232: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +232: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +232: 2# RDInfoTheory::InfoBitRanker::getTopN(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu//lib/libRDKitInfoTheory.so.1 +232: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so +232: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so +232: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +232: 6# 0x00007F13C736866C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +232: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +232: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +232: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +232: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +232: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu/rdkit/rdBase.so +232: 12# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +232: 13# 0x00007F13C7365406 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +232: 14# _PyObject_MakeTpCall in /usr/bin/python3 +232: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 +232: 16# 0x00000000005BEE79 in /usr/bin/python3 +232: 17# _PyEval_EvalFrameDefault in /usr/bin/python3 +232: 18# 0x0000000000547080 in /usr/bin/python3 +232: 19# 0x00000000006AB720 in /usr/bin/python3 +232: 20# _PyObject_MakeTpCall in /usr/bin/python3 +232: 21# _PyEval_EvalFrameDefault in /usr/bin/python3 +232: 22# 0x00000000005BEE79 in /usr/bin/python3 +232: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 +232: 24# 0x0000000000547080 in /usr/bin/python3 +232: 25# 0x00000000006AB720 in /usr/bin/python3 +232: 26# _PyObject_MakeTpCall in /usr/bin/python3 +232: 27# _PyEval_EvalFrameDefault in /usr/bin/python3 +232: 28# 0x00000000005BEE79 in /usr/bin/python3 +232: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +232: 30# 0x0000000000547080 in /usr/bin/python3 +232: 31# 0x00000000006AB720 in /usr/bin/python3 +232: 32# _PyObject_MakeTpCall in /usr/bin/python3 +232: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 +232: 34# 0x000000000059582E in /usr/bin/python3 +232: 35# _PyObject_MakeTpCall in /usr/bin/python3 +232: 36# _PyEval_EvalFrameDefault in /usr/bin/python3 +232: 37# PyEval_EvalCode in /usr/bin/python3 +232: 38# 0x000000000066A861 in /usr/bin/python3 +232: 39# 0x000000000066670C in /usr/bin/python3 +232: 40# 0x000000000067F713 in /usr/bin/python3 +232: 41# 0x000000000067ECE3 in /usr/bin/python3 +232: 42# 0x000000000067EB1E in /usr/bin/python3 +232: 43# Py_RunMain in /usr/bin/python3 +232: 44# Py_BytesMain in /usr/bin/python3 +232: 45# 0x00007F13C8A06D68 in /lib/x86_64-linux-gnu/libc.so.6 +232: 46# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +232: 47# _start in /usr/bin/python3 +232: ---------- +232: **** +232: +215/235 Test #222: pyMolProcessing ........................ Passed 3.22 sec +test 235 + Start 235: pythonProjectTests + +235: Test command: /usr/bin/python3 "-m" "pytest" +235: Working Directory: /build/reproducible-path/rdkit-202409.6/Projects +235: Test timeout computed to be: 1500 +232: ... +232: ---------------------------------------------------------------------- +232: Ran 5 tests in 0.150s +232: +232: OK +211: ........[09:21:50] Explicit valence for atom # 1 O, 3, is greater than permitted +216/235 Test #232: pyRanker ............................... Passed 1.63 sec +228: ..... +228: ---------------------------------------------------------------------- +228: Ran 5 tests in 1.970s +228: +228: OK +234: .. +234: ---------------------------------------------------------------------- +234: Ran 2 tests in 0.034s +234: +234: OK +234: Testing ChemicalFeatures Wrapper code: +211: .. +211: ---------------------------------------------------------------------- +211: Ran 38 tests in 11.786s +211: +211: OK +211: done +217/235 Test #228: pyMatCalc .............................. Passed 3.54 sec +218/235 Test #234: pyFeatures ............................. Passed 1.78 sec +219/235 Test #211: pyMolStandardize ....................... Passed 12.57 sec +220/235 Test #198: pyTestThreads .......................... Passed 26.16 sec +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 58.01 seconds +221/235 Test #163: testFMCS ............................... Passed 58.20 sec +231: ....... +231: ---------------------------------------------------------------------- +231: Ran 11 tests in 3.917s +231: +231: OK +222/235 Test #231: pySimDivPickers ........................ Passed 5.01 sec +173: Query 1 +235: ============================= test session starts ============================== +235: platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 +235: rootdir: /build/reproducible-path/rdkit-202409.6/Projects +235: configfile: pytest.ini +235: plugins: typeguard-4.4.2 +235: collected 12 items +235: +221: Randomness seeded to: 1169995654 +221: =============================================================================== +221: All tests passed (203 assertions in 1 test case) +221: +223/235 Test #221: testMolProcessing ...................... Passed 11.04 sec +150: --------------------------------- +150: test O3A multithreading bug +150: +150: --------------------------------- +150: testCrippenO3A multithreading +150: +150: generating reference data +150: processing +150: launch :0 +150: launch :1 +150: launch :2 +150: launch :3 +148: .........[09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +148: [09:22:03] Molecule does not have explicit Hs. Consider calling AddHs() +173: Query 2 +184: ............. +184: ---------------------------------------------------------------------- +184: Ran 19 tests in 55.134s +184: +184: OK +184: Testing atom rings +184: testing bond rings +184: searching atom rings +184: searching bond rings +184: done +224/235 Test #184: pySubstructLibrary ..................... Passed 56.72 sec 148: ... 148: ---------------------------------------------------------------------- -148: Ran 22 tests in 40.172s +148: Ran 22 tests in 93.227s +148: +148: OK +225/235 Test #148: pyDistGeomHelpers ...................... Passed 95.44 sec +170: [09:22:19] Timed out after 71 seconds. +209: [09:22:44] Explicit valence for atom # 0 Br, 1, is greater than permitted 209: =============================================================================== 209: All tests passed (38344 assertions in 51 test cases) 209: -148: -148: OK -224/235 Test #209: molStandardizeCatchTest ................ Passed 34.88 sec -225/235 Test #148: pyDistGeomHelpers ...................... Passed 41.07 sec -173: Query 2 -33: [12:01:40] Finished -33: [12:01:40] ------------------------------------- -33: [12:01:40] Test github1843: RWMol.clear() should not destroy ring pointer. -33: [12:01:40] Finished -33: [12:01:40] ------------------------------------- -33: [12:01:40] Test Github 6370: non-physical radical counts being preserved -33: [12:01:40] Finished -226/235 Test #33: graphmolTest1 .......................... Passed 45.52 sec -147: [12:01:50] UFFTYPER: Unrecognized atom type: S_6+6 (0) -147: [12:01:50] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -147: [12:01:50] UFFTYPER: Unrecognized charge state for atom: 0 +226/235 Test #209: molStandardizeCatchTest ................ Passed 66.52 sec +147: [09:22:53] UFFTYPER: Unrecognized atom type: S_6+6 (0) +147: [09:22:53] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +147: [09:22:53] UFFTYPER: Unrecognized charge state for atom: 0 150: --------------------------------- 150: test getO3AForProbeConfs 150: 150: *********************************************************** -227/235 Test #150: testO3AAlign ........................... Passed 54.25 sec +227/235 Test #150: testO3AAlign ........................... Passed 130.70 sec 235: DbCLI/UnitTestDbCLI.py ............ [100%] 235: 235: =============================== warnings summary =============================== @@ -35184,38 +35224,33 @@ 235: decBase = declarative_base() 235: 235: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -235: ======================== 12 passed, 1 warning in 45.18s ======================== -228/235 Test #235: pythonProjectTests ..................... Passed 46.66 sec -184: ............. -184: ---------------------------------------------------------------------- -184: Ran 19 tests in 55.436s -184: -184: OK -184: Testing atom rings -184: testing bond rings -184: searching atom rings -184: searching bond rings -184: done -229/235 Test #184: pySubstructLibrary ..................... Passed 55.94 sec -146: [12:02:18] done -146: [12:02:18] --------------------------------- -146: [12:02:18] test github issue 256: handling of zero-atom molecules +235: ================== 12 passed, 1 warning in 100.32s (0:01:40) =================== +228/235 Test #235: pythonProjectTests ..................... Passed 103.62 sec +173: Query 3 +170: =============================================================================== +170: All tests passed (3582 assertions in 34 test cases) +170: +229/235 Test #170: testRascalMCES ......................... Passed 165.20 sec +146: [09:23:43] done +171: =============================================================================== +171: All tests passed (93 assertions in 5 test cases) +171: +230/235 Test #171: testRascalCluster ...................... Passed 168.17 sec +173: Query 4 +146: [09:23:43] --------------------------------- +146: [09:23:43] test github issue 256: handling of zero-atom molecules 146: -146: [12:02:18] --------------------------------- -146: [12:02:18] test embedder callback function -146: [12:02:18] --------------------------------- -146: [12:02:18] test multi-threaded multi-conf embedding +146: [09:23:43] --------------------------------- +146: [09:23:43] test embedder callback function +146: [09:23:43] --------------------------------- +146: [09:23:43] test multi-threaded multi-conf embedding 146: -146: [12:02:24] --------------------------------- -146: [12:02:24] test github issue 563: Incorrect ring stereochemistry after embedding +146: [09:23:54] --------------------------------- +146: [09:23:54] test github issue 563: Incorrect ring stereochemistry after embedding 146: 146: CNC[C@H]1CC[C@H](C[NH3+])CC1 -171: =============================================================================== -171: All tests passed (93 assertions in 5 test cases) -171: -230/235 Test #171: testRascalCluster ...................... Passed 88.55 sec -146: [12:02:26] --------------------------------- -146: [12:02:26] test github issue 568: Incorrect stereochemistry after embedding +146: [09:23:58] --------------------------------- +146: [09:23:58] 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 @@ -35226,7 +35261,16 @@ 146: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC -147: [12:02:30] Interrupted, cancelling conformer generation +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 +173: Query 5 +146: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 +146: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 +146: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 +146: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 +146: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O +146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O +147: [09:24:28] 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] @@ -35259,26 +35303,20 @@ 147: 13 7->5 order: 1 147: 14 8->12 order: a conj?: 1 aromatic?: 1 147: 15 11->2 order: 1 stereo: CCW bonds: (9 4 5) conj?: 1 +146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 147: =============================================================================== 147: All tests passed (12742 assertions in 21 test cases) 147: -231/235 Test #147: distGeomHelpersCatch ................... Passed 94.04 sec -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 -173: Query 3 -146: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 -146: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 -146: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 -146: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 -170: =============================================================================== -170: All tests passed (3582 assertions in 34 test cases) -170: -232/235 Test #170: testRascalMCES ......................... Passed 100.14 sec -173: Query 4 -146: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 -146: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O -146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O -146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O +231/235 Test #147: distGeomHelpersCatch ................... Passed 226.65 sec 146: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 +33: [09:24:31] Finished +33: [09:24:31] ------------------------------------- +33: [09:24:31] Test github1843: RWMol.clear() should not destroy ring pointer. +33: [09:24:31] Finished +33: [09:24:31] ------------------------------------- +33: [09:24:31] Test Github 6370: non-physical radical counts being preserved +33: [09:24:31] Finished +232/235 Test #33: graphmolTest1 .......................... Passed 247.03 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 @@ -35288,2738 +35326,79 @@ 146: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 146: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 146: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] -173: Query 5 -146: [12:03:01] Molecule does not have explicit Hs. Consider calling AddHs() -146: [12:02:53] --------------------------------- -146: [12:02:53] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system -146: [12:02:53] --------------------------------- -146: [12:02:53] More ChEMBL molecules failing bounds smoothing. -146: [12:02:54] --------------------------------- -146: [12:02:54] ugly conformations can be generated for highly constrained ring systems. -146: [12:02:54] --------------------------------- -146: [12:02:54] test embed parameters structure. -146: [12:02:54] --------------------------------- -146: [12:02:54] test github 1227: Hs being used in RMSD filtering. -146: [12:02:54] --------------------------------- -146: [12:02:54] Failure to embed larger aromatic rings. -146: [12:02:56] --------------------------------- -146: [12:02:56] Deterministic with large random seeds -146: [12:02:59] --------------------------------- -146: [12:02:59] Github #1990: seg fault after RemoveHs -146: [12:03:00] --------------------------------- -146: [12:03:00] Github #2246: Use coordMap when starting embedding from random coords -146: [12:03:01] --------------------------------- -146: [12:03:01] Providing a distance bounds matrix. -146: [12:03:01] --------------------------------- -146: [12:03:01] Disabling fragmentation. -146: [12:03:01] --------------------------------- -146: [12:03:01] Using symmetry in conformation pruning. -146: [12:03:01] --------------------------------- -146: [12:03:01] Force trans amides. -146: [12:03:01] --------------------------------- -146: [12:03:01] test missing Hs warning. -146: [12:03:01] --------------------------------- -146: [12:03:01] basic H bond support. -146: [12:03:01] ******************************************************* -233/235 Test #146: testDistGeomHelpers .................... Passed 125.23 sec +146: [09:25:06] Molecule does not have explicit Hs. Consider calling AddHs() 173: =============================================================================== 173: All tests passed (215 assertions in 18 test cases) 173: -234/235 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 151.96 sec -5: [12:05:42] Finished: testMultipleTimes() -5: [12:05:42] -5: ----------------------------------------- -235/235 Test #5: testConcurrentQueue .................... Passed 288.10 sec - -100% tests passed, 0 tests failed out of 235 - -Total Test time (real) = 288.26 sec -make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' - create-stamp debian/debhelper-build-stamp - dh_testroot -O--buildsystem=cmake - dh_prep -O--buildsystem=cmake - dh_installdirs -O--buildsystem=cmake - debian/rules override_dh_auto_install -make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6' -dh_auto_install - cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/rdkit-202409.6/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" -make[2]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -/usr/bin/cmake -S/build/reproducible-path/rdkit-202409.6 -B/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 -make -f CMakeFiles/Makefile2 preinstall -make[3]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -make[3]: Nothing to be done for 'preinstall'. -make[3]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' -Install the project... -/usr/bin/cmake -P cmake_install.cmake --- Install configuration: "None" --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDRandom.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemdraw.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/cactvs.py --- Installing: 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/entropy.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitRank.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitClusterer.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/VoteImg.py --- Installing: 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Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterUtils.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Murtagh.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Standardize.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Butina.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgeom.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgen.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfdoc.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfmetrics.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pidPDF.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfutils.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/pidReportLab.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/HTMLPiddler.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/psmetrics.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/fontinfo.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/latin1MetricsCache.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/pidPS.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pid.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/pidtest.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/pstests.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/testallps.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/pidSVG.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/pidPyart.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/Fontmapping.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/utils.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/stringformat.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/colors.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pidPIL.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pagesizes.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt4.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/formatted-strings.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK/pidTK.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWX.py --- 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--- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/TopNContainer.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/LazySignature.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitUtils.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsemble.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsembleDb.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Avalon --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Avalon/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/pytest.ini --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Transform.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Supply.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Node.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesSupply.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/demo.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbMolSupply.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SDSupply.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Output.py --- Installing: 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/SimilarityPickers.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/__init__.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/DTDs --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt --- 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/SmartsLib --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz --- 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/rddata.sql --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/Salts.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/struchk --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt --- Installing: 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/index.rst --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/introduction_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_38.png --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_26.png --- Installing: 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3w2c_N15.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/BEG_test.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/JVE_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/AKI_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i24_1C9.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/lig_crystal_aligned.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dpv.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb --- Installing: 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3m11_AKI.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/README.md --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/BEG.png --- Installing: 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NP_Score/publicnp.model.gz --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NP_Score/npscorer.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/testData --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/pbf.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/PBF/README --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/MolVS --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/MolVS/molvs_cli.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/IFG --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/IFG/README --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score/build_sascore_db.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/LEF --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/atomcontrib.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/data --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query.smi --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/final_fraggle_results.csv --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/fragmentation_tversky_out --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/ChEMBL_11265_actives.smi --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query_fragmentation.csv --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/fraggle.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/cxn_tversky.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/rdkit_tversky.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/fraggle/readme.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/pzc --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.html --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/pzc/readme.md --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/sdf2smi.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/cdk2.sdf --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fastcluster.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered.tsv --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/cdk2.smi --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_rfrag.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_output.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_smi_output.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample.smi --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym.csv --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mol_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_default.csv --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks_mol_trans.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_smarts_output.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxratio.csv --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs_smarts.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_fragmented.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smiles_mol_trans.smi --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_transfroms.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans_smarts.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_smi.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_smart_output.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/indexing.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/search_mmp_db.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/rfrag.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/mol_transform.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/mmpa/create_mmp_db.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test.cpp --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/CMakeLists.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/CMakeLists.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/testConformerParser.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/rdConformerParser.cpp --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.cpp --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/requirements.txt --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810.smi --- Installing: 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/README.md --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/.gitignore --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/CACHEDIR.TAG --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache/stepwise --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache/nodeids 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/build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Numerics/SymmMatrix.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Numerics/Vector.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Numerics/Conrec.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceField.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceField.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceField.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/Contrib.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/ForceField.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/AngleConstraint.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/AngleConstraints.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/DistanceConstraint.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/DistanceConstraints.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/PositionConstraint.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/TorsionConstraint.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleBend.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/BondStretch.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Contribs.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/DistanceConstraint.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/AngleConstraint.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionConstraint.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/PositionConstraint.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Nonbonded.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Params.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Utils.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Inversion.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/Inversions.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/UFF/TorsionAngle.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleBend.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/BondStretch.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/StretchBend.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/OopBend.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionAngle.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/Nonbonded.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/Contribs.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/DistanceConstraint.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/AngleConstraint.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/TorsionConstraint.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/PositionConstraint.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ForceField/MMFF/Params.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField/rdForceField.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeometry.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeometry.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeometry.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/BoundsMatrix.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/ChiralSet.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/ChiralViolationContrib.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/ChiralViolationContribs.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/DistGeomUtils.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/DistViolationContrib.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/DistViolationContribs.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/FourthDimContrib.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/FourthDimContribs.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DistGeom/TriangleSmooth.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry/DistGeom.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCatalogs.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCatalogs.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCatalogs.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Catalogs/CatalogEntry.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Catalogs/Catalog.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Catalogs/CatalogParams.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGraphMol.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGraphMol.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGraphMol.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Atom.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/atomic_data.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/AtomIterators.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Atropisomers.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Bond.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/BondIterators.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Canon.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Chirality.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Conformer.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/details.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/GraphMol.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolOps.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolPickler.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/PeriodicTable.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/QueryAtom.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/QueryBond.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/QueryOps.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RDKitBase.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RDKitQueries.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Resonance.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RingInfo.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Rings.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ROMol.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RWMol.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SanitException.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SubstanceGroup.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/StereoGroup.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MonomerInfo.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/new_canon.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolBundle.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSmilesParse.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSmilesParse.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSmilesParse.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmartsWrite.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParse.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesParseOps.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/SmilesWrite.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SmilesParse/CanonicalizeStereoGroups.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDepictor.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDepictor.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDepictor.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Depictor/DepictUtils.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Depictor/EmbeddedFrag.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Depictor/RDDepictor.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdDepictor.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMarvinParser.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMarvinParser.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMarvinParser.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MarvinParse/MarvinParser.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFileParsers.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFileParsers.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFileParsers.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/CDXMLParser.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParsers.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileParserUtils.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolFileStereochem.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/FileWriters.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolSupplier.v1API.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MolWriters.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceParsers.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/SequenceWriters.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/GeneralFileReader.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedMolSupplier.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/MultithreadedSDMolSupplier.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FileParsers/PNGParser.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructMatch.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructMatch.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructMatch.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Substruct/SubstructUtils.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGenericGroups.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGenericGroups.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGenericGroups.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/GenericGroups/GenericGroups.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemReactions.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemReactions.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemReactions.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Reaction.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionParser.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionPickler.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionFingerprints.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionUtils.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/ReactionRunner.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/PreprocessRxn.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/SanitizeRxn.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/Enumerate.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateBase.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerateTypes.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/CartesianProduct.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSample.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemReactions/Enumerate/RandomSampleAllBBs.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdChemReactions.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemTransforms.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemTransforms.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemTransforms.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTautomerQuery.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTautomerQuery.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/TautomerQuery/TautomerQuery.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdTautomerQuery.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubgraphs.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubgraphs.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubgraphs.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/Subgraphs.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Subgraphs/SubgraphUtils.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFilterCatalog.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFilterCatalog.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalogEntry.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterCatalog.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatcherBase.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FilterMatchers.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdfiltercatalog.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFragCatalog.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFragCatalog.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFragCatalog.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogEntry.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatalogUtils.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatGenerator.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragCatParams.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FragCatalog/FragFPGenerator.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdfragcatalog.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDescriptors.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDescriptors.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDescriptors.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Crippen.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/BCUT.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Lipinski.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolSurf.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/ConnectivityDescriptors.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MQN.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RegisterDescriptor.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Property.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR2D.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/Data3Ddescriptors.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolData3Ddescriptors.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/USRDescriptor.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AtomFeat.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/OxidationNumbers.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/DCLV.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MolDescriptors3D.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/EEM.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PBF.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/PMI.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/AUTOCORR3D.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/RDF.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/MORSE.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/GETAWAY.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/WHIM.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Descriptors/CoulombMat.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolDescriptors.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFingerprints.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFingerprints.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFingerprints.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairs.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/Fingerprints.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MorganFingerprints.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MACCS.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MHFP.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/FingerprintGenerator.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/AtomPairGenerator.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/MorganGenerator.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/RDKitFPGenerator.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/TopologicalTorsionGenerator.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Fingerprints/FingerprintUtil.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdFingerprintGenerator.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMHFPFingerprint.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitPartialCharges.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitPartialCharges.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitPartialCharges.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerCharges.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/PartialCharges/GasteigerParams.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdPartialCharges.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolTransforms.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolTransforms.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolTransforms.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolTransforms/MolTransforms.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolTransforms.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitForceFieldHelpers.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/FFConvenience.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/AtomTyper.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/Builder.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/UFF/UFF.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/Builder.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/MMFF/MMFF.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdForceFieldHelpers.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDistGeomHelpers.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/DistGeomHelpers/Embedder.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdDistGeom.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolAlign.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolAlign.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolAlign.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitO3AAlign.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitO3AAlign.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitO3AAlign.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/AlignMolecules.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolAlign/O3AAlignMolecules.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolAlign.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolChemicalFeatures.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/FeatureParser.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolChemicalFeatures/MolChemicalFeature.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolChemicalFeatures.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitShapeHelpers.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitShapeHelpers.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeEncoder.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ShapeHelpers/ShapeUtils.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdShapeHelpers.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolCatalog.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolCatalog.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolCatalog.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogEntry.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalog.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolCatalog/MolCatalogParams.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolCatalog.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2D.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2Dwx.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DJS.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DHelpers.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolDraw2D.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolDraw2D.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolDraw2D/MolDraw2DCairo.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/rdMolDraw2D.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFMCS.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFMCS.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitFMCS.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FMCS/FMCS.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/FMCS/Graph.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdFMCS.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolHash.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolHash.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolHash.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolHash/MolHash.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolHash/nmmolhash.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolHash.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMMPA.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMMPA.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMMPA.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MMPA/MMPA.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMMPA.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRascalMCES.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRascalMCES.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRascalMCES.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalMCES.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalOptions.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalClusterOptions.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RascalMCES/RascalResult.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdRascalMCES.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSynthonSpaceSearch.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSynthonSpaceSearch.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpace.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSet.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/Synthon.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SearchResults.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdSynthonSpaceSearch.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCIPLabeler.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitCIPLabeler.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/CIPLabeler/CIPLabeler.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/CIPLabeler/TooManyNodesException.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdCIPLabeler.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDeprotect.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDeprotect.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitDeprotect.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Deprotect/Deprotect.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdDeprotect.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitReducedGraphs.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitReducedGraphs.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ReducedGraphs/ReducedGraphs.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdReducedGraphs.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTrajectory.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTrajectory.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitTrajectory.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Snapshot.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Trajectory/Trajectory.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructLibrary.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSubstructLibrary.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrary.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/SubstructLibrarySerialization.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SubstructLibrary/PatternFactory.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdSubstructLibrary.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitRGroupDecomposition.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecomp.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/RGroupDecomposition/RGroupDecompParams.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdRGroupDecomposition.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInterchange.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInterchange.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInterchange.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/MolInterchange.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolInterchange/details.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolInterchange.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSLNParse.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSLNParse.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSLNParse.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNAttribs.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParse.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/SLNParse/SLNParseOps.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdSLNParse.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdchem.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdmolops.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdqueries.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdmolfiles.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdtrajectory.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolStandardize.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolStandardize.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolStandardize.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Pipeline.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/MolStandardize.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Metal.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Normalize.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Validate.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Charge.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Tautomer.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/Fragment.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolStandardize/rdMolStandardize.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitScaffoldNetwork.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/ScaffoldNetwork/ScaffoldNetwork.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Scaffolds/rdScaffoldNetwork.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolEnumerator.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolEnumerator.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/MolEnumerator.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolEnumerator/LinkNode.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolEnumerator.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitAbbreviations.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitAbbreviations.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitAbbreviations.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/Abbreviations/Abbreviations.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdAbbreviations.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitGeneralizedSubstruct.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/GeneralizedSubstruct/XQMol.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdGeneralizedSubstruct.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolProcessing.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolProcessing.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolProcessing.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolProcessing/MolProcessing.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMolProcessing.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInteractionFields.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInteractionFields.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitMolInteractionFields.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/GraphMol/MolInteractionFields/MIFDescriptors.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdMIF.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/AndQuery.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/EqualityQuery.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/GreaterEqualQuery.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/GreaterQuery.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/LessEqualQuery.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/LessQuery.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/NullQueryAlgebra.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/OrQuery.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/Query.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/QueryObjects.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/RangeQuery.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/SetQuery.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Query/XOrQuery.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/Features/Feature.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricFuncs.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/DataManip/MetricMatrixCalc/MetricMatrixCalc.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataManip/Metric/rdMetricMatrixCalc.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSimDivPickers.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitSimDivPickers.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/SimDivPickers/DistPicker.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/SimDivPickers/LeaderPicker.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/SimDivPickers/HierarchicalClusterPicker.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/SimDivPickers/MaxMinPicker.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/rdSimDivPickers.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKithc.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKithc.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKithc.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Clustering.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitInfoTheory.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitInfoTheory.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitInfoTheory.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/rdInfoTheory.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/cQuantize.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1.2024.09.6 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemicalFeatures.so.1 --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/libRDKitChemicalFeatures.so --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ChemicalFeatures/ChemicalFeature.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/include/rdkit/ChemicalFeatures/FreeChemicalFeature.h --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/rdChemicalFeatures.so - -===================================================================== -PostgreSQL cartridge installation succeeded. -===================================================================== -Restart the PostgreSQL service before using the PostgreSQL -RDKit cartridge. -===================================================================== - --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDPaths.py --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets.cmake --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkit/rdkit-targets-none.cmake --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkit/rdkit-config.cmake --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkit/rdkit-config-version.cmake --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-targets.cmake --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-targets-none.cmake --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-config.cmake --- Installing: /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/cmake/rdkitpython/rdkitpython-config-version.cmake +146: [09:24:51] --------------------------------- +146: [09:24:51] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system +146: [09:24:51] --------------------------------- +146: [09:24:51] More ChEMBL molecules failing bounds smoothing. +146: [09:24:51] --------------------------------- +146: [09:24:51] ugly conformations can be generated for highly constrained ring systems. +146: [09:24:51] --------------------------------- +146: [09:24:51] test embed parameters structure. +146: [09:24:51] --------------------------------- +146: [09:24:51] test github 1227: Hs being used in RMSD filtering. +146: [09:24:51] --------------------------------- +146: [09:24:51] Failure to embed larger aromatic rings. +146: [09:24:57] --------------------------------- +146: [09:24:57] Deterministic with large random seeds +146: [09:25:03] --------------------------------- +146: [09:25:03] Github #1990: seg fault after RemoveHs +146: [09:25:03] --------------------------------- +146: [09:25:03] Github #2246: Use coordMap when starting embedding from random coords +146: [09:25:06] --------------------------------- +146: [09:25:06] Providing a distance bounds matrix. +146: [09:25:06] --------------------------------- +146: [09:25:06] Disabling fragmentation. +146: [09:25:06] --------------------------------- +146: [09:25:06] Using symmetry in conformation pruning. +146: [09:25:06] --------------------------------- +146: [09:25:06] Force trans amides. +146: [09:25:06] --------------------------------- +146: [09:25:06] test missing Hs warning. +146: [09:25:06] --------------------------------- +146: [09:25:06] basic H bond support. +146: [09:25:06] ******************************************************* +233/235 Test #146: testDistGeomHelpers .................... Passed 264.47 sec +234/235 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 240.66 sec +235/235 Test #5: testConcurrentQueue ....................***Timeout 1500.06 sec +[09:20:23] +----------------------------------------- +[09:20:23] Finished: testPushAndPop() +[09:20:23] +----------------------------------------- +[09:20:23] +----------------------------------------- + + +99% tests passed, 1 tests failed out of 235 + +Total Test time (real) = 1500.48 sec + +The following tests FAILED: + 5 - testConcurrentQueue (Timeout) +Errors while running CTest +make[2]: *** [Makefile:94: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-x86_64-linux-gnu' +dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 returned exit code 2 +make[1]: *** [debian/rules:149: override_dh_auto_test] Error 25 make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' - debian/rules override_dh_install -make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6' -mkdir -p /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3 -mv /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13/site-packages /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3/dist-packages -rm -f -rf /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3.13 -ln -sf /usr/share/fonts/truetype/freefont/FreeSans.ttf /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/FreeSans.ttf -dh_install -ppython3-rdkit /usr/lib/python3 -rm -f -rf /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/lib/python3/dist-packages/rdkit/docs/ -rm -f -rf /build/reproducible-path/rdkit-202409.6/debian/tmp/usr/share/RDKit/Projects/__pycache__ -dh_numpy3 -dh_install -for v in $(pg_buildext supported-versions); do \ - mkdir -p debian/postgresql-$v-rdkit/usr/lib/postgresql/$v/lib/ debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ - cp Code/PgSQL/rdkit/build-$v/librdkit.so debian/postgresql-$v-rdkit/usr/lib/postgresql/$v/lib/rdkit.so; \ - cp Code/PgSQL/rdkit/build-$v/rdkit*.sql debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ - cp Code/PgSQL/rdkit/build-$v/update_sql/rdkit*.sql debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ - cp Code/PgSQL/rdkit/rdkit.control debian/postgresql-$v-rdkit/usr/share/postgresql/$v/extension/; \ -done -mkdir -p /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit/ -# cp /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/latex/RDKit.pdf /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit/ -cp -a /build/reproducible-path/rdkit-202409.6/Docs/Book/_build/html /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit/ -ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit//html/cppapi/jquery.js -ln -sf /usr/share/javascript/jquery/jquery.js /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/jquery.js -ln -sf /usr/share/javascript/underscore/underscore.js /build/reproducible-path/rdkit-202409.6/debian/rdkit-doc/usr/share/doc/rdkit//html/_static/underscore.js -make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' - dh_installdocs -O--buildsystem=cmake - debian/rules override_dh_installchangelogs -make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6' -dh_installchangelogs ReleaseNotes.md -make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' - debian/rules override_dh_python3 -make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6' -dh_python3 -ppython3-rdkit -I: dh_python3 fs:421: renaming rdBase.so to rdBase.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming DistGeom.so to DistGeom.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdGeometry.so to rdGeometry.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdAbbreviations.so to rdAbbreviations.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdChemReactions.so to rdChemReactions.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdChemicalFeatures.so to rdChemicalFeatures.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdCoordGen.so to rdCoordGen.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdDepictor.so to rdDepictor.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdDeprotect.so to rdDeprotect.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdDistGeom.so to rdDistGeom.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdFMCS.so to rdFMCS.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdFingerprintGenerator.so to rdFingerprintGenerator.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdForceFieldHelpers.so to rdForceFieldHelpers.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdGeneralizedSubstruct.so to rdGeneralizedSubstruct.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMHFPFingerprint.so to rdMHFPFingerprint.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMIF.so to rdMIF.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMMPA.so to rdMMPA.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMolAlign.so to rdMolAlign.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMolCatalog.so to rdMolCatalog.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMolChemicalFeatures.so to rdMolChemicalFeatures.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMolDescriptors.so to rdMolDescriptors.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMolEnumerator.so to rdMolEnumerator.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMolHash.so to rdMolHash.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMolInterchange.so to rdMolInterchange.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMolProcessing.so to rdMolProcessing.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMolTransforms.so to rdMolTransforms.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdPartialCharges.so to rdPartialCharges.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdRGroupDecomposition.so to rdRGroupDecomposition.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdRascalMCES.so to rdRascalMCES.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdReducedGraphs.so to rdReducedGraphs.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdSLNParse.so to rdSLNParse.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdShapeHelpers.so to rdShapeHelpers.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdSubstructLibrary.so to rdSubstructLibrary.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdSynthonSpaceSearch.so to rdSynthonSpaceSearch.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdTautomerQuery.so to rdTautomerQuery.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdchem.so to rdchem.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdfiltercatalog.so to rdfiltercatalog.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdfragcatalog.so to rdfragcatalog.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdinchi.so to rdinchi.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdmolfiles.so to rdmolfiles.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdmolops.so to rdmolops.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdqueries.so to rdqueries.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdtrajectory.so to rdtrajectory.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMolStandardize.so to rdMolStandardize.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming Clustering.so to Clustering.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdForceField.so to rdForceField.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-313-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-313-x86_64-linux-gnu.so -dh_numpy3 -ppython3-rdkit -make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' - dh_installsystemduser -O--buildsystem=cmake - dh_lintian -O--buildsystem=cmake - dh_perl -O--buildsystem=cmake - dh_link -O--buildsystem=cmake - dh_strip_nondeterminism -O--buildsystem=cmake - dh_compress -O--buildsystem=cmake - dh_fixperms -O--buildsystem=cmake - debian/rules override_dh_missing -make[1]: Entering directory '/build/reproducible-path/rdkit-202409.6' -dh_missing --list-missing -dh_missing: warning: usr/lib/postgresql/17/lib/rdkit.so exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/BackwardsIncompatibleChanges.md exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/CMakeLists.txt exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/FindMyRDKit.cmake exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example1.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example10.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example11.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example12.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example13.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example14.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example15.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example16.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example17.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example2.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example3.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example4.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example5.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example6.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example7.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example8.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/C++Examples/example9.cpp exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/Cartridge.md exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/Cookbook.rst exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/GettingStartedInC++.md exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/GettingStartedInPython.rst exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/GettingStartedWithContributing.md exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/Install.md exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/Makefile exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/Overview.md exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/RDKit_Book.rst exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/api-docs.rst exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/conf.py exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/AmideBond.rxn exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/MinimalFeatures.fdef exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/README.md exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/bzr.sdf exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/bzr.smi exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/cdk2.sdf exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/chiral.mol exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/input.mol exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/invalid.mol exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/s1p_chembldoc89753.txt exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/solubility.test.sdf exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/solubility.train.sdf exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Book/data/test_multi_colours.py exists in 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usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/Notebooks/compounds.txt exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Docs/RD.css exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/README.md exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Scripts/FeatFinderCLI.py exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Scripts/PythonFormat.py exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Scripts/README.md exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Scripts/create_deb_packages.sh exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Scripts/gen_rdkit_stubs/__init__.py exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Scripts/gen_rdkit_stubs/__main__.py exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Scripts/gen_rdkit_stubs/worker.py exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Scripts/patch_rdkit_docstrings/__init__.py exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Scripts/patch_rdkit_docstrings/__main__.py exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Scripts/patch_rdkit_docstrings/clang_worker.py exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/Scripts/test.sh exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/RDKit/license.txt exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/postgresql/17/extension/rdkit--3.8--4.0.sql exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.0--4.0.1.sql exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.0.1--4.1.sql exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.1--4.1.1.sql exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.1.1--4.2.sql exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.2--4.3.0.sql exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.3.0--4.4.0.sql exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.4.0--4.5.0.sql exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.5.0--4.6.0.sql exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.6.0--4.6.1.sql exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/postgresql/17/extension/rdkit--4.6.1.sql exists in debian/tmp but is not installed to anywhere -dh_missing: warning: usr/share/postgresql/17/extension/rdkit.control exists in debian/tmp but is not installed to anywhere - The following debhelper tools have reported what they installed (with files per package) - * dh_install: librdkit-dev (64), librdkit1t64 (124), postgresql-17-rdkit (0), python3-rdkit (1), rdkit-data (3), rdkit-doc (0) - * dh_installdocs: librdkit-dev (0), librdkit1t64 (0), postgresql-17-rdkit (0), python3-rdkit (0), rdkit-data (0), rdkit-doc (0) - If the missing files are installed by another tool, please file a bug against it. - When filing the report, if the tool is not part of debhelper itself, please reference the - "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). - (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.md.gz) - Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built - If the omission is intentional or no other helper can take care of this consider adding the - paths to debian/not-installed. -make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' - dh_dwz -a -O--buildsystem=cmake - dh_strip -a -O--buildsystem=cmake - dh_makeshlibs -a -O--buildsystem=cmake - dh_shlibdeps -a -O--buildsystem=cmake -dpkg-shlibdeps: warning: diversions involved - output may be incorrect - diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 -dpkg-shlibdeps: warning: diversions involved - output may be incorrect - diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged -dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol byteaout: it's probably a plugin -dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: diversions involved - output may be incorrect - diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 -dpkg-shlibdeps: warning: diversions involved - output may be incorrect - diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged - dh_installdeb -O--buildsystem=cmake - dh_gencontrol -O--buildsystem=cmake -dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined -dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined -dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined - dh_md5sums -O--buildsystem=cmake - dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202409.6-2_amd64.deb'. -dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202409.6-2_amd64.deb'. -dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202409.6-2_all.deb'. -dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202409.6-2_amd64.deb'. -dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202409.6-2_all.deb'. -dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202409.6-2_amd64.deb'. -dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202409.6-2_amd64.deb'. -dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202409.6-2_amd64.deb'. -dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202409.6-2_amd64.deb'. - dpkg-genbuildinfo --build=binary -O../rdkit_202409.6-2_amd64.buildinfo - dpkg-genchanges --build=binary -O../rdkit_202409.6-2_amd64.changes -dpkg-genchanges: info: binary-only upload (no source code included) - dpkg-source --after-build . -dpkg-buildpackage: info: binary-only upload (no source included) -dpkg-genchanges: info: not including original source code in upload +make: *** [debian/rules:46: binary] Error 2 +dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration +E: Failed autobuilding of package +I: user script /srv/workspace/pbuilder/423878/tmp/hooks/C01_cleanup starting +debug output: disk usage on i-capture-the-hostname at Wed Mar 12 19:45:30 UTC 2025 +Filesystem Size Used Avail Use% Mounted on +tmpfs 40G 0 40G 0% /dev/shm + +I: user script /srv/workspace/pbuilder/423878/tmp/hooks/C01_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/3959858 and its subdirectories -I: Current time: Tue Apr 14 12:11:44 -12 2026 -I: pbuilder-time-stamp: 1776211904 +I: removing directory /srv/workspace/pbuilder/423878 and its subdirectories