Diff of the two buildlogs: -- --- b1/build.log 2025-09-09 15:43:57.750042605 +0000 +++ b2/build.log 2025-09-09 17:00:35.243962581 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Sep 9 03:21:14 -12 2025 -I: pbuilder-time-stamp: 1757431274 +I: Current time: Tue Oct 13 12:07:01 +14 2026 +I: pbuilder-time-stamp: 1791842821 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -36,53 +36,85 @@ dpkg-source: info: applying better_enums.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/988309/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1070101/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 Oct 12 22:07 /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/1070101/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1070101/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=40 ' - DISTRIBUTION='forky' - 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(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=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='150a5b03713549408d8956bc26b080a6' - 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='988309' - PS1='# ' - PS2='> ' + INVOCATION_ID=81bddc50ee7c4b7dae7e6fc4f0c8894c + 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=1070101 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.AD3V4xWq/pbuilderrc_1DDZ --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AD3V4xWq/b1 --logfile b1/build.log rdkit_202503.1-5.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.AD3V4xWq/pbuilderrc_cbjU --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AD3V4xWq/b2 --logfile b2/build.log rdkit_202503.1-5.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/988309/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1070101/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -583,7 +615,7 @@ Get: 376 http://deb.debian.org/debian forky/main amd64 texlive-latex-recommended all 2025.20250727-3 [8454 kB] Get: 377 http://deb.debian.org/debian forky/main amd64 texlive-pictures all 2025.20250727-3 [22.1 MB] Get: 378 http://deb.debian.org/debian forky/main amd64 texlive-latex-extra all 2025.20250727-3 [27.4 MB] -Fetched 434 MB in 6s (66.9 MB/s) +Fetched 434 MB in 15s (28.1 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 ... 19898 files and directories currently installed.) @@ -1798,8 +1830,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Sep 9 15:23:21 UTC 2025. -Universal Time is now: Tue Sep 9 15:23:21 UTC 2025. +Local time is now: Mon Oct 12 22:11:03 UTC 2026. +Universal Time is now: Mon Oct 12 22:11:03 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-4.2) ... @@ -2190,7 +2222,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202503.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rdkit_202503.1-5_source.changes +I: user script /srv/workspace/pbuilder/1070101/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1070101/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202503.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rdkit_202503.1-5_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202503.1-5 dpkg-buildpackage: info: source distribution unstable @@ -2314,8 +2350,8 @@ command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (1.9s) --- Generating done (1.2s) +-- Configuring done (15.0s) +-- Generating done (11.5s) CMake Warning: Manually-specified variables were not used by the project: @@ -2376,14 +2412,14 @@ command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (0.6s) +-- Configuring done (5.4s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/build-17 make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' dh_auto_build - cd obj-x86_64-linux-gnu && make -j40 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202503.1 -B/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -2391,114 +2427,114 @@ make[3]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/INCHI-API /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/RDGeneral/versions.cpp [ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o -[ 1%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/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 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/IntegerStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/ga/IntegerStringChromosomePolicy.cpp -[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/RDGeneral/LocaleSwitcher.cpp -cd /build/reproducible-path/rdkit-202503.1/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 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/StringChromosome.cpp.o -MF CMakeFiles/ga.dir/ga/StringChromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/StringChromosome.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/GA/ga/StringChromosome.cpp [ 2%] Built target inchi_support +[ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o +cd /build/reproducible-path/rdkit-202503.1/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 -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-Dhc_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o -MF CMakeFiles/hc.dir/hc.c.o.d -o CMakeFiles/hc.dir/hc.c.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/Cluster/Murtagh/hc.c [ 3%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202503.1/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 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target hc -[ 3%] Linking CXX static library librdkitCatch.a -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake [ 3%] Linking CXX shared library ../../lib/libRDKitga.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDStreams.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2025.03.1 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/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 @@ -2513,146 +2549,146 @@ [ 3%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend -make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd 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Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.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-202503.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/RDBoost /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake "--color=" -make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral 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"--color=" make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/ExplicitBitVect.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 3%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o -[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -[ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o +[ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -[ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o +[ 4%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o +[ 4%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -MF CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o.d -o CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/RDGeneral/testConcurrentQueue.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost && /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 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DiscreteValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/DiscreteValueVect.cpp -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/FPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/FPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/FPBReader.cpp -cd /build/reproducible-path/rdkit-202503.1/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 -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/HierarchicalClusterPicker.cpp -cd /build/reproducible-path/rdkit-202503.1/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 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/build/reproducible-path/rdkit-202503.1/Code/DataStructs/MultiFPBReader.cpp +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/Numerics/testMatrices.cpp cd /build/reproducible-path/rdkit-202503.1/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 -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/MaxMinPicker.cpp -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Query/CMakeFiles/testQuery.dir/test.cpp.o -MF CMakeFiles/testQuery.dir/test.cpp.o.d -o CMakeFiles/testQuery.dir/test.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Query/test.cpp -[ 5%] Linking CXX executable testConcurrentQueue -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConcurrentQueue.dir/link.txt --verbose=1 [ 6%] Linking CXX executable testMatCalc cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 6%] Built target testMatCalc +[ 6%] Linking CXX executable testConcurrentQueue +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/EigenSolvers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 @@ -2675,29 +2711,22 @@ cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/SimDivPickers/testPickers.cpp [ 6%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 -[ 6%] Linking CXX executable logTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 6%] Built target Catalogs +[ 6%] Linking CXX executable logTestsCatch +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 6%] Built target logTestsCatch [ 6%] Linking CXX executable testMatrices cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 -[ 6%] Linking CXX executable testQuery -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 6%] Built target testMatrices -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 6%] Built target testQuery [ 6%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 -[ 6%] Linking CXX executable dictTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -2705,198 +2734,217 @@ make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.dir/depend +make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/Geometry /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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/build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake "--color=" -make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' 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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/catchDataStructs.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build -make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build -make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make 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Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/Geometry/point.cpp +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -MF CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o.d -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/testDatastructs.cpp [ 6%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o [ 6%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -[ 6%] Building CXX object 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -MF CMakeFiles/testFPB.dir/testFPB.cpp.o.d -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/testFPB.cpp -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -[ 6%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o +[ 6%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o cd 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -MF CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o.d -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DataStructs/testMultiFPB.cpp -cd /build/reproducible-path/rdkit-202503.1/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 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/pickersTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/catch_tests.cpp -cd /build/reproducible-path/rdkit-202503.1/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 -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/UniformRealValueGrid3D.cpp +[ 6%] Linking CXX executable dictTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 +[ 6%] Linking CXX executable testQuery +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/ML/Data/cQuantize.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testRDValue.dir/link.d CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 8%] Built target testRDValue -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKithc.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 8%] Built target pickersTestsCatch [ 8%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 -[ 8%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 8%] 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[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' 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 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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/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -MF CMakeFiles/rdGeometry.dir/Point.cpp.o.d -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/Wrap/Point.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 9%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/catch_tests.cpp +[ 9%] Building CXX object 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/FreeChemicalFeature.cpp [ 9%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -[ 9%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o [ 9%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Geometry/CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -MF CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o.d -o CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/testRealValueGrid.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Geometry/Wrap/UniformRealValueGrid3D.cpp +cd /build/reproducible-path/rdkit-202503.1/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 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CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolPickler.cpp +[ 11%] Linking CXX executable testMultiFPB +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testMultiFPB.dir/link.d CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 11%] Built target testMultiFPB [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 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-DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/AtomIterators.cpp.o -MF CMakeFiles/GraphMol.dir/AtomIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/AtomIterators.cpp -[ 11%] Linking CXX shared library ../../../lib/libRDKitAlignment.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 -[ 11%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so -cd /build/reproducible-path/rdkit-202503.1/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Alignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2025.03.1 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 11%] Built target Alignment [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ 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Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -MF CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/BondIterators.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2025.03.1 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2025.03.1 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 11%] Built target ChemicalFeatures [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Aromaticity.cpp.o -MF CMakeFiles/GraphMol.dir/Aromaticity.cpp.o.d -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Aromaticity.cpp /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': @@ -3020,166 +3115,107 @@ | ~~~~~~~~~~~~~^~~ [ 11%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 -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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake "--color=" +[ 11%] Linking CXX executable geometryTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 /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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 11%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp +[ 11%] Built target rdMetricMatrixCalc [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o.d -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ConjugHybrid.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 /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.1.2025.03.1 /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 -[ 11%] Linking CXX executable testMultiFPB +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/geometryTestsCatch.dir/link.d CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 -[ 11%] Built target rdMetricMatrixCalc +[ 11%] Built target geometryTestsCatch [ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/AddHs.cpp.o -MF CMakeFiles/GraphMol.dir/AddHs.cpp.o.d -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/AddHs.cpp +[ 11%] Linking CXX executable testRealValueGrid +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script 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-[ 15%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/cQuantize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -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 +[ 15%] Built target testConrec +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION 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/usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 15%] Built target cQuantize +[ 15%] Built target rdSimDivPickers +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolProps.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 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Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 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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 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 17%] Built target rdGeometry [ 17%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 /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.1.2025.03.1 /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 @@ -3193,168 +3229,168 @@ [ 17%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make 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Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/tableTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend +make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 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cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake "--color=" cd 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object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o +[ 20%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o +[ 20%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/SmilesWrite.cpp +[ 20%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o cd /build/reproducible-path/rdkit-202503.1/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 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CIPMol.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/CIPMol.cpp -[ 18%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Mancude.cpp +cd /build/reproducible-path/rdkit-202503.1/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 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/SLNParse/SLNAttribs.cpp +cd /build/reproducible-path/rdkit-202503.1/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 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/sln.tab.cpp +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/GasteigerParams.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/GasteigerParams.cpp [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp -[ 21%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/sln.tab.cpp.o -MF CMakeFiles/SLNParse.dir/sln.tab.cpp.o.d -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/sln.tab.cpp [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Rule1a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp -[ 21%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ 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Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -MF CMakeFiles/SLNParse.dir/lex.yysln.cpp.o.d -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/lex.yysln.cpp [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Rule1b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o @@ -3363,25 +3399,25 @@ cd /build/reproducible-path/rdkit-202503.1/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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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 22%] Linking CXX executable tableTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/tableTestsCatch.dir/link.txt --verbose=1 [ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o cd 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Rule5.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule5.cpp -[ 22%] Built target tableTestsCatch +[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Rule6.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule6.cpp [ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-Wextra -fPIC -Wl,--dependency-file=CMakeFiles/PartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -3392,10 +3428,10 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' -[ 22%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 [ 22%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o cd /build/reproducible-path/rdkit-202503.1/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 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-Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -3426,14 +3462,14 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 22%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/BFGSOpt.cpp.o -MF CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o.d -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer/BFGSOpt.cpp [ 22%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Wrap/Trajectory.cpp +[ 22%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Wrap/rdTrajectory.cpp +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Wrap/Trajectory.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Subgraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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 @@ -3453,93 +3489,71 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ForceField /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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/build/reproducible-path/rdkit-202503.1/Code/ForceField/ForceField.cpp -[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/AngleConstraint.cpp +[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/DistanceConstraint.cpp -[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/ForceField/DistanceConstraints.cpp +[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o +[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o +[ 25%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so +[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/PositionConstraint.cpp.o -MF 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/TorsionConstraint.cpp +[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/UFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/AngleBend.cpp -[ 24%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/UFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/BondStretch.cpp cd /build/reproducible-path/rdkit-202503.1/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 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/Inversions.cpp -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/UFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF/TorsionAngle.cpp cd /build/reproducible-path/rdkit-202503.1/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 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object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o +[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o +[ 25%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 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CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -3551,8 +3565,6 @@ cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 26%] Built target GenericGroups -[ 26%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp 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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake "--color=" @@ -3560,23 +3572,47 @@ 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-202503.1/obj-x86_64-linux-gnu' [ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Substruct/SubstructMatch.cpp [ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Substruct/SubstructMatch.cpp cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Substruct/SubstructUtils.cpp +[ 26%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 26%] 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-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 26%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o +[ 26%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ShapeEncoder.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp +[ 26%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp [ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 -[ 26%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdPartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 26%] Built target rdPartialCharges [ 26%] Linking CXX executable testOptimizer cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2025.03.1 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2025.03.1 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testOptimizer.dir/link.d CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' [ 26%] Built target testOptimizer +[ 26%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2025.03.1 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2025.03.1 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 26%] Built target SLNParse make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend @@ -3587,6 +3623,16 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 26%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp +[ 26%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdqueries.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 26%] Built target rdqueries +[ 26%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdtrajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 26%] Built target rdtrajectory [ 26%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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 @@ -3601,29 +3647,24 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 26%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp -[ 26%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 -[ 26%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 [ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdtrajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/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-202503.1/obj-x86_64-linux-gnu' /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdCIPLabeler.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdqueries.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 26%] Built target rdCIPLabeler -[ 26%] Built target rdqueries -[ 26%] Built target rdtrajectory [ 26%] Linking CXX shared library ../../lib/libRDKitForceField.so cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 26%] Built target ForceField +[ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 26%] Built target rdMolCatalog [ 26%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 -[ 26%] Built target ForceField /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2025.03.1 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -3638,11 +3679,6 @@ cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp [ 26%] Linking CXX shared module ../../../rdkit/rdBase.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 -[ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 26%] Built target rdMolCatalog /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdBase.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -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-202503.1/obj-x86_64-linux-gnu' [ 26%] Built target rdBase @@ -3653,335 +3689,320 @@ [ 27%] Built target rdSLNParse [ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 -[ 28%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 /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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 28%] Built target rdMolTransforms +[ 28%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o CMakeFiles/SmilesParse.dir/SmilesJSONParsers.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.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 28%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 [ 28%] Built target SmilesParse make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend 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 -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/queryTestsCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' 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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/queryTestsCatch.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.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 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build +make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' 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Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build -make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f 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Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o +make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o -[ 28%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/graphmolIterTest.dir/itertest.cpp.o -MF CMakeFiles/graphmolIterTest.dir/itertest.cpp.o.d -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/itertest.cpp [ 28%] Building CXX object Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -[ 28%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o [ 28%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o -MF CMakeFiles/smiTest2.dir/test2.cpp.o.d -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse/test2.cpp -[ 28%] Building CXX object Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/graphmolMemTest1.dir/memtest1.cpp.o -MF CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o.d -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/memtest1.cpp cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/molbundleTestsCatch.dir/catch_molbundle.cpp.o -MF CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o.d -o CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/catch_molbundle.cpp 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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/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-202503.1/Code/GraphMol/PartialCharges/test1.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 28%] Built target SubstructMatch make -f 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/FragCatalogEntry.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/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 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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/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/FragCatGenerator.cpp -[ 32%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD 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CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp [ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 -[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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queryTestsCatch -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/graphmolMemTest1.dir/link.d CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganFingerprints.cpp -[ 33%] Built target graphmolMemTest1 +[ 32%] Built target rdShapeHelpers +[ 32%] Building CXX object 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp +[ 33%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/FilterMatchers.cpp +[ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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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/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -MF CMakeFiles/Fingerprints.dir/MHFP.cpp.o.d -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MHFP.cpp [ 33%] Built target graphmolcpTest -[ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 -DRDK_BUILD_THREADSAFE_SSS 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Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp -[ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/MorganGenerator.cpp -[ 34%] Linking CXX executable molbundleTestsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molbundleTestsCatch.dir/link.txt --verbose=1 -[ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 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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/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp -[ 34%] Linking CXX executable testSubgraphs2 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp +[ 33%] Linking CXX executable queryTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/queryTestsCatch.dir/link.txt --verbose=1 +[ 33%] Linking CXX executable moliteratorTestsCatch cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script 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directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 33%] Built target queryTestsCatch /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/moliteratorTestsCatch.dir/link.d CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -o moliteratorTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 34%] Built target moliteratorTestsCatch -[ 34%] Linking CXX executable testSubgraphs1 -cd /build/reproducible-path/rdkit-202503.1/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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testSubgraphs1.dir/link.d CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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 +[ 33%] Linking CXX executable graphmolIterTest +[ 33%] Built target moliteratorTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 +[ 34%] Linking CXX executable v2smiTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2smiTestCatch.dir/link.txt --verbose=1 +[ 34%] Linking CXX executable graphmolMemTest1 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/graphmolIterTest.dir/link.d CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/graphmolMemTest1.dir/link.d CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 34%] Built target testSubgraphs1 +[ 34%] Built target graphmolMemTest1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 34%] Built target v2smiTestCatch +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 34%] Built target graphmolIterTest [ 34%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2025.03.1 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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 @@ -3989,43 +4010,46 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 34%] Built target ReducedGraphs make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend -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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake "--color=" +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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 34%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -[ 34%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/test1.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 34%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -MF CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o.d -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp +[ 34%] Linking CXX executable testSubgraphs2 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testSubgraphs2.dir/link.d CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 34%] Built target testSubgraphs2 +[ 34%] Linking CXX executable molbundleTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molbundleTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/molbundleTestsCatch.dir/link.d CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -o molbundleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 34%] Built target molbundleTestsCatch +[ 34%] Linking CXX executable testSubgraphs1 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs1.dir/link.txt --verbose=1 [ 34%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testSubgraphs1.dir/link.d CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 34%] Built target testSubgraphs1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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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 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2025.03.1 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 34%] Built target FragCatalog -[ 34%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2025.03.1 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 34%] 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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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/build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp +[ 34%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -4033,51 +4057,49 @@ make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/depend make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make 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/build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build -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]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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 -f 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Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/ForceField/Wrap/ForceField.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInteractionFields_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERACTIONFIELDS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/MIFDescriptors.cpp +[ 34%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o +[ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/TriangleSmooth.cpp.o -MF CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o.d -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/TriangleSmooth.cpp -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/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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&& /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ChiralViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/ChiralViolationContribs.cpp -[ 35%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 +cd /build/reproducible-path/rdkit-202503.1/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 -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp +[ 35%] Building CXX object Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB 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../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -4085,31 +4107,48 @@ 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[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/CoordGen/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build +make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make 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Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o +[ 36%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Templates.cpp.o -MF CMakeFiles/Depictor.dir/Templates.cpp.o.d -o CMakeFiles/Depictor.dir/Templates.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Templates.cpp -[ 36%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o +[ 36%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o cd /build/reproducible-path/rdkit-202503.1/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 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../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 36%] Built target testReducedGraphs [ 36%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 [ 36%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 -[ 36%] Linking CXX executable graphmolqueryTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 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../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2025.03.1 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -4117,21 +4156,18 @@ make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend make[4]: 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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/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp -[ 36%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 36%] Built target FilterCatalog @@ -4145,11 +4181,6 @@ cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp [ 36%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp -[ 36%] Linking CXX executable testReducedGraphs -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testReducedGraphs.dir/link.d CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 36%] Built target testReducedGraphs [ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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 @@ -4164,31 +4195,28 @@ 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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' 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-202503.1/obj-x86_64-linux-gnu' +[ 36%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 36%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o [ 36%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp -[ 36%] Linking CXX executable ForceFieldsCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 36%] Built target ForceFieldsCatch -[ 36%] Linking CXX executable testSLNParse -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/graphmolqueryTest.dir/link.d CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 36%] Built target testSLNParse +[ 36%] Built target graphmolqueryTest [ 36%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 +[ 36%] Linking CXX executable ForceFieldsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DistGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2025.03.1 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -4197,30 +4225,38 @@ 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 '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DistGeom /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/DistGeom /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 36%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o [ 36%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Embedder.cpp +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/BoundsMatrixBuilder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp [ 36%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB 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Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/Wrap/DistGeom.cpp +[ 36%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Embedder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Embedder.cpp [ 36%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/DistGeom/testDistGeom.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 36%] Built target ForceFieldsCatch +[ 36%] Linking CXX executable testSLNParse +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testSLNParse.dir/link.d CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 36%] Built target testSLNParse [ 36%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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 @@ -4235,31 +4271,31 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 36%] Building CXX object Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolInteractionFields/Wrap/rdMIF.cpp +[ 36%] Linking CXX executable testDistGeom +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 [ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 36%] Built target rdForceFieldHelpers -[ 36%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 [ 37%] Linking CXX executable smaTest1 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 -[ 37%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so -cd 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../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -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 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../lib/libRDKitForceField.so.1.2025.03.1 ../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 37%] Built target testDistGeom +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 37%] Built target rdForceFieldHelpers /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 37%] Built target rdCoordGen [ 37%] Built target smaTest1 +[ 37%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202503.1/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 37%] Built target rdMolChemicalFeatures -[ 37%] Linking CXX executable testDistGeom -cd /build/reproducible-path/rdkit-202503.1/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 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../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 +[ 37%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -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-202503.1/obj-x86_64-linux-gnu' -[ 37%] Built target testDistGeom +[ 37%] Built target rdCoordGen [ 37%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2025.03.1 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o CMakeFiles/Depictor.dir/Templates.cpp.o /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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 @@ -4268,57 +4304,57 @@ [ 37%] 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 -make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/External/INCHI-API /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API/CMakeFiles/RDInchiLib.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f External/INCHI-API/CMakeFiles/RDInchiLib.dir/build.make External/INCHI-API/CMakeFiles/RDInchiLib.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build -make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 38%] Building CXX object External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o +[ 38%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/CMakeFiles/RDInchiLib.dir/inchi.cpp.o -MF CMakeFiles/RDInchiLib.dir/inchi.cpp.o.d -o CMakeFiles/RDInchiLib.dir/inchi.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/INCHI-API/inchi.cpp +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f 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-Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdAbbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 39%] Built target rdAbbreviations -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 39%] Built target rdForceField +[ 39%] Built target DistGeom [ 39%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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 @@ -4363,15 +4399,15 @@ /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/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-202503.1/obj-x86_64-linux-gnu' [ 39%] Built target rdMIF +[ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 [ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 39%] Built target rdDepictor -[ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 39%] Built target rdDepictor [ 39%] Built target rdFingerprintGenerator [ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 @@ -4390,67 +4426,67 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' +[ 39%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o [ 39%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -[ 39%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -[ 39%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FileParsers/CDXMLParser.cpp cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SDMolSupplier.cpp [ 40%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o +[ 40%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o +cd 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SmilesWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SmilesWriter.cpp +cd /build/reproducible-path/rdkit-202503.1/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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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/TplFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/TplFileParser.cpp +[ 40%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o [ 40%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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/SDWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SDWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SDWriter.cpp -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SequenceParsers.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SequenceParsers.cpp -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB 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-I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SVGParser.cpp.o -MF CMakeFiles/FileParsers.dir/SVGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/SVGParser.cpp -cd /build/reproducible-path/rdkit-202503.1/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 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+[ 42%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp [ 42%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdinchi.dir/link.txt --verbose=1 @@ -4469,528 +4505,486 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 42%] 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Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend -make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend +make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/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 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake "--color=" 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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/canonTestsCatch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend -make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake "--color=" +make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/depend -make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend -make -f Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build.make Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/depend -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/canonTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend -make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend -make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend +make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend -make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake "--color=" +make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build +make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake "--color=" -make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build -make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build +make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build +make -f Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build.make Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/depend +make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/build.make 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build -make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build +make -f 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o -MF CMakeFiles/testCoordGen.dir/test.cpp.o.d -o CMakeFiles/testCoordGen.dir/test.cpp.o -c /build/reproducible-path/rdkit-202503.1/External/CoordGen/test.cpp +make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build make -f 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/build make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build +make -f Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 42%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/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-202503.1/Code/ForceField/UFF/testUFFForceField.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 42%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/molopstest.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testSGroup.dir/testSGroup.cpp.o -MF CMakeFiles/testSGroup.dir/testSGroup.cpp.o.d -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/testSGroup.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build +make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/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-202503.1/Code/ForceField/UFF/testUFFForceField.cpp -[ 42%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o +make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/hanoiTest.dir/hanoitest.cpp.o -MF CMakeFiles/hanoiTest.dir/hanoitest.cpp.o.d -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/hanoitest.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/DaylightParser.cpp -[ 45%] Linking CXX executable testMol2ToMol -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/CDXMLParser.cpp +[ 46%] Linking CXX executable testTplParser +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolOrganometallicsCatch.dir/link.txt --verbose=1 +[ 46%] Built target testSquiggleDoubleBonds +[ 46%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 45%] Built target testMultithreadedMolSupplier -[ 45%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -cd 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/build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 45%] Built target XYZFileParserCatchTest -[ 45%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionUtils.cpp -[ 45%] Linking CXX executable testAtropisomers -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAtropisomers.dir/link.txt --verbose=1 -[ 46%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 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Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp +[ 46%] Linking CXX executable graphmolOrganometallicsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolOrganometallicsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 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/build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FileParsers/file_parsers_catch.cpp +[ 46%] Linking CXX executable testMultithreadedMolSupplier +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 +[ 46%] Linking CXX executable testAtropisomers +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/ReactionRunner.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testMultithreadedMolSupplier.dir/link.d CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu 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/usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 47%] Built target molopsTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make 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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-202503.1/obj-x86_64-linux-gnu' -[ 47%] Built target nontetrahedralCatch -make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FileParsers/v2_suppliers_catch.cpp [ 48%] Linking CXX executable testGeneralFileReader cd /build/reproducible-path/rdkit-202503.1/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++ 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Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FileParsers/v2_suppliers_catch.cpp +[ 48%] Linking CXX executable molopsTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molopsTestsCatch.dir/link.txt --verbose=1 +[ 48%] Linking CXX executable graphmoltestPicklerGlobalSetting +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' -[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -cd 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct/test1.cpp -[ 48%] Linking CXX executable graphmolAdjustQueryCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.dir/link.txt --verbose=1 +[ 48%] Linking CXX executable pickleTestsCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 48%] Built target graphmolAdjustQueryCatch +[ 48%] Built target hanoiTest make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake "--color=" @@ -5010,8 +5006,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 48%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection 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/usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 -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-202503.1/obj-x86_64-linux-gnu' +[ 48%] Built target testCoordGen make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake "--color=" @@ -5028,145 +5032,153 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 48%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd 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-c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MolSurf.cpp +[ 48%] Built target testExtendedStereoParsing make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testFingerprints.dir/test1.cpp.o -MF CMakeFiles/testFingerprints.dir/test1.cpp.o.d -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/test1.cpp -[ 50%] Linking CXX executable cdxmlParserCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 +[ 48%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code 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CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/connectTheDotsTest.dir/link.d CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 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Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 50%] Built target cdxmlParserCatchTest -[ 50%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp -[ 50%] Linking CXX executable testMolWriter -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 -[ 50%] Linking CXX executable multithreadedSupplierCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/multithreadedSupplierCatchTest.dir/link.txt --verbose=1 -[ 51%] Linking CXX executable testSGroup -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 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-o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/BCUT.cpp +[ 48%] Linking CXX executable canonTestsCatch +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/graphmolAdjustQueryCatch.dir/link.d CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MQN.cpp.o -MF CMakeFiles/Descriptors.dir/MQN.cpp.o.d -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/MQN.cpp -[ 51%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp +[ 49%] Linking CXX executable testDepictor +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 +[ 49%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/AtomFeat.cpp.o -MF CMakeFiles/Descriptors.dir/AtomFeat.cpp.o.d -o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/AtomFeat.cpp -[ 52%] Linking CXX executable testMMFFForceField -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DCLV.cpp.o -MF CMakeFiles/Descriptors.dir/DCLV.cpp.o.d -o CMakeFiles/Descriptors.dir/DCLV.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/DCLV.cpp +[ 51%] Built target testMHFPFingerprint +[ 51%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/catch_tests.cpp make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/depend make[4]: Entering directory 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/USRDescriptor.cpp +[ 51%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 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Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o +[ 51%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 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executable filterCatalogTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/filterCatalogTest.dir/link.d CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 53%] Built target filterCatalogTest -[ 53%] Building CXX object 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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/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -MF CMakeFiles/Descriptors.dir/EEM.cpp.o.d -o CMakeFiles/Descriptors.dir/EEM.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/EEM.cpp +[ 52%] Built target filterCatalogTest +[ 52%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DCLV.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DCLV.cpp.o -MF CMakeFiles/Descriptors.dir/DCLV.cpp.o.d -o CMakeFiles/Descriptors.dir/DCLV.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/DCLV.cpp make -f 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp +[ 52%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && 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-[ 56%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o +[ 57%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202503.1/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 -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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/build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 substructTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/substructTestCatch.dir/link.d CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch 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directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 57%] Built target molTransformsTestCatch -[ 57%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -MF CMakeFiles/FMCS.dir/FMCS.cpp.o.d -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/FMCS.cpp +[ 57%] Linking CXX executable testMolTransforms +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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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-202503.1/obj-x86_64-linux-gnu' +[ 57%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o +[ 57%] Built target forceFieldHelpersCatch +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/catch_tests.cpp -[ 57%] Linking CXX executable substructTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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 testSubstructMatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 +[ 57%] Built target testMolTransforms +[ 57%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp +[ 57%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp +[ 57%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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_iostreams.so.1.83.0 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 57%] Built target forceFieldHelpersCatch -[ 57%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp -[ 57%] Linking CXX executable testMMFFForceFieldHelpersMultiThread +[ 57%] Built target testSubstructMatch +[ 58%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FMCS/SubstructMatchCustom.cpp +[ 58%] Linking CXX executable testMMFFForceFieldHelpersMultiThread cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/substructTestCatch.dir/link.d CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 57%] Built target substructTestCatch -[ 57%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Seed.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testMMFFForceFieldHelpersMultiThread.dir/link.d CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 57%] Linking CXX executable testMolTransforms -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 -[ 57%] Built target testMMFFForceFieldHelpersMultiThread +[ 58%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend -[ 57%] Linking CXX executable testCrystalForceField make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 57%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o +[ 58%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /build/reproducible-path/rdkit-202503.1/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 -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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-Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCrystalForceField.dir/link.d CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 57%] Built target testCrystalForceField -[ 57%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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 +[ 58%] Linking CXX executable graphmoltestChirality +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 +[ 58%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 57%] Built target testMolTransforms -[ 58%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/FMCS/SubstructMatchCustom.cpp +[ 58%] Built target graphmoltestChirality make -f Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/DependInfo.cmake "--color=" @@ -5462,8 +5493,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/RascalMCES/RascalMCES.cpp -[ 58%] Linking CXX executable fpGenTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 +[ 58%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/AtomSymbol.cpp.o -MF CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/AtomSymbol.cpp +[ 58%] Linking CXX executable testCrystalForceField +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake "--color=" @@ -5472,155 +5505,140 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/PositionVariation.cpp -[ 58%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolEnumerator/RepeatUnit.cpp -[ 59%] Linking CXX executable testShapeHelpers -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 -[ 59%] Linking CXX 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 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-fcf-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/fpGenTestCatch.dir/link.d CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 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/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp -[ 59%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/AtomSymbol.cpp.o -MF CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/AtomSymbol.cpp -[ 59%] Linking CXX executable testChemTransforms -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 -[ 59%] Linking CXX executable molAlignCatchTest -cd 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolEnumerator/RepeatUnit.cpp +[ 60%] Linking CXX executable fpTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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molAlignCatchTest +[ 60%] Built target testShapeHelpers make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake "--color=" +[ 60%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ 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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/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Deprotect.cpp -[ 59%] Linking CXX executable fpTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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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-D_FORTIFY_SOURCE=2 -Wdate-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-202503.1/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp -[ 61%] Linking CXX executable testMMFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 -[ 61%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem 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Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 62%] Building CXX object 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CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/RascalMCES/PartitionSet.cpp +[ 60%] Linking CXX executable molAlignCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 +[ 60%] Linking CXX executable testMolCatalog +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 +[ 60%] Linking CXX executable testMMFFForceFieldHelpers +cd 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&& /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp -[ 62%] Linking CXX shared library ../../../lib/libRDKitMMPA.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 -[ 62%] Linking CXX executable smiTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/test1.cpp -[ 62%] Linking CXX executable testFingerprintGenerators -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/DrawTextJS.cpp make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 62%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o +[ 61%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External 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/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-202503.1/obj-x86_64-linux-gnu' +[ 62%] Built target testFingerprintGenerators +[ 62%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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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/testFeatures.dir/link.d CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 62%] Built target testFeatures +[ 62%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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-I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Wrap/MolOps.cpp make -f Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o -MF CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o.d -o CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/MolProcessing.cpp -[ 65%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp make -f Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/build.make Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2025.03.1 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 66%] Built target Deprotect +[ 66%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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-MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp -[ 66%] Linking CXX shared library ../../../lib/libRDKitFMCS.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 +[ 66%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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/usr/lib/x86_64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 66%] Built target testFingerprints +[ 66%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp -[ 67%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -cd 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../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 68%] Built target chiralityTestsCatch -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend +[ 66%] Built target MolEnumerator +make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build +make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 68%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolEnumerator/enumerator_catch.cpp +[ 66%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -MF CMakeFiles/FMCStest.dir/testFMCS.cpp.o.d -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Test/testFMCS.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolProcessing.so.1 -o ../../../lib/libRDKitMolProcessing.so.1.2025.03.1 CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitRDStreams.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolProcessing.so.1.2025.03.1 ../../../lib/libRDKitMolProcessing.so.1 ../../../lib/libRDKitMolProcessing.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 68%] Built target MolProcessing +[ 66%] Built target MolProcessing +[ 66%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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-ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../lib/libRDKitAlignment.so.1.2025.03.1 ../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 66%] Built target graphmolTestsCatch +[ 67%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp +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-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' 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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake "--color=" +[ 67%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolEnumerator/enumerator_catch.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make 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CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp +[ 67%] Linking CXX executable molInterchangeCatchTest +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -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 +[ 67%] Linking CXX shared library ../../../lib/libRDKitDetermineBonds.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DetermineBonds && /usr/bin/cmake -E cmake_link_script CMakeFiles/DetermineBonds.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DetermineBonds.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDetermineBonds.so.1 -o ../../../lib/libRDKitDetermineBonds.so.1.2025.03.1 CMakeFiles/DetermineBonds.dir/DetermineBonds.cpp.o ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DetermineBonds && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDetermineBonds.so.1.2025.03.1 ../../../lib/libRDKitDetermineBonds.so.1 ../../../lib/libRDKitDetermineBonds.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 68%] Built target testMMPA -[ 68%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/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-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp -[ 68%] Linking CXX executable molInterchangeTest1 +[ 67%] Built target DetermineBonds +[ 67%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp +[ 67%] Linking CXX executable molInterchangeTest1 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp +[ 67%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp +[ 68%] Linking CXX executable testMMPA +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testMMPA.dir/link.d 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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/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp -[ 69%] Built target testAbbreviations -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test 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/usr/lib/x86_64-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DetermineBonds && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDetermineBonds.so.1.2025.03.1 ../../../lib/libRDKitDetermineBonds.so.1 ../../../lib/libRDKitDetermineBonds.so +[ 69%] Building CXX object Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 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../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 69%] Built target DetermineBonds -[ 69%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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-202503.1/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp -[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp +[ 69%] Built target testAbbreviations make -f Code/GraphMol/DetermineBonds/CMakeFiles/determineBondsCatchTest.dir/build.make Code/GraphMol/DetermineBonds/CMakeFiles/determineBondsCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DetermineBonds /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DetermineBonds 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-fPIC -std=gnu++17 -MD -MT Code/GraphMol/DetermineBonds/CMakeFiles/determineBondsCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/determineBondsCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/determineBondsCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DetermineBonds/catch_tests.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o 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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 +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1 ../../../lib/libRDKitRascalMCES.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 69%] Built target RascalMCES make -f Code/GraphMol/DetermineBonds/Wrap/CMakeFiles/rdDetermineBonds.dir/build.make Code/GraphMol/DetermineBonds/Wrap/CMakeFiles/rdDetermineBonds.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DetermineBonds/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DetermineBonds/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DetermineBonds/Wrap/CMakeFiles/rdDetermineBonds.dir/DependInfo.cmake "--color=" -[ 70%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/RascalMCES.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/DetermineBonds/Wrap/CMakeFiles/rdDetermineBonds.dir/build.make Code/GraphMol/DetermineBonds/Wrap/CMakeFiles/rdDetermineBonds.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 70%] Building CXX object Code/GraphMol/DetermineBonds/Wrap/CMakeFiles/rdDetermineBonds.dir/rdDetermineBonds.cpp.o +[ 69%] Building CXX object Code/GraphMol/DetermineBonds/Wrap/CMakeFiles/rdDetermineBonds.dir/rdDetermineBonds.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DetermineBonds/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDetermineBonds_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/DetermineBonds/Wrap/CMakeFiles/rdDetermineBonds.dir/rdDetermineBonds.cpp.o -MF CMakeFiles/rdDetermineBonds.dir/rdDetermineBonds.cpp.o.d -o CMakeFiles/rdDetermineBonds.dir/rdDetermineBonds.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DetermineBonds/Wrap/rdDetermineBonds.cpp -[ 71%] Linking CXX executable fileParsersTest1 -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 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Linking CXX shared library ../../../lib/libRDKitDescriptors.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 71%] Built target RascalMCES -[ 71%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. 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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-202503.1/obj-x86_64-linux-gnu' -[ 71%] Built target testMolProcessing +[ 70%] Built target testMolProcessing make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 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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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Descriptors/testGETAWAY.cpp make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -6138,7 +6174,7 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o +[ 70%] Building CXX object 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-fcf-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-202503.1/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-202503.1/obj-x86_64-linux-gnu' @@ -6146,7 +6182,7 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu' -[ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o +[ 70%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Descriptors/testCoulombMat.cpp 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-202503.1/obj-x86_64-linux-gnu' @@ -6154,489 +6190,489 @@ make[4]: Leaving 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/DependInfo.cmake "--color=" make[4]: Leaving directory 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp -[ 71%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 -[ 71%] Linking CXX shared module ../../../../rdkit/Chem/rdMolProcessing.so -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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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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.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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 cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so +[ 71%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 71%] Built target MolDraw2D make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make 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/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 72%] Built target rdDetermineBonds +[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK 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-std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/catch_tests.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 72%] Built target rdMolEnumerator +[ 72%] Linking CXX executable testRascalCluster +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 72%] Built target testRascalCluster +[ 72%] Linking CXX executable testATF +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testATF.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testATF.dir/link.d CMakeFiles/testATF.dir/testATF.cpp.o -o testATF 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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-202503.1/obj-x86_64-linux-gnu' [ 72%] Built target testATF -[ 72%] Linking CXX executable testRascalCluster -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 -[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 -[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdDetermineBonds.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DetermineBonds/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDetermineBonds.dir/link.txt --verbose=1 [ 72%] Linking CXX executable testBCUT cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1=. -fstack-protector-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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../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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 +[ 72%] Built target testBCUT +[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdMolProcessing.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitRDStreams.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 72%] Built target testRascalCluster -[ 72%] Built target rdDeprotect -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testBCUT.dir/link.d CMakeFiles/testBCUT.dir/testBCUT.cpp.o -o testBCUT ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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 +[ 72%] Built target rdMolProcessing +[ 72%] Linking CXX executable testCoulombMat +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 +[ 72%] Linking CXX executable testAUTOCORR2D +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR2D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testCoulombMat.dir/link.d CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdDetermineBonds.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDetermineBonds.so CMakeFiles/rdDetermineBonds.dir/rdDetermineBonds.cpp.o ../../../../lib/libRDKitDetermineBonds.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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 +[ 72%] Built target testCoulombMat +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testAUTOCORR2D.dir/link.d CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 72%] Built target testBCUT -[ 72%] Built target rdDetermineBonds +[ 72%] Linking CXX executable testRDF +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDF.dir/link.txt --verbose=1 +[ 72%] Built target testAUTOCORR2D +[ 72%] Linking CXX executable testGETAWAY +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGETAWAY.dir/link.txt --verbose=1 [ 73%] Linking CXX executable testEEM cd 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../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 73%] Built target testRDF +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testGETAWAY.dir/link.d CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -o testGETAWAY ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 73%] Built target testGETAWAY [ 73%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so cd /build/reproducible-path/rdkit-202503.1/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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testWHIM.dir/link.d CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so 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-fcf-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.1.2025.03.1 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 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/usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 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../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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 +[ 75%] Linking CXX executable testPBF +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPBF.dir/link.txt --verbose=1 +[ 75%] Linking CXX executable testAUTOCORR3D +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR3D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testPBF.dir/link.d CMakeFiles/testPBF.dir/testPBF.cpp.o -o testPBF ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 75%] Built target graphmolMolOpsTest -[ 75%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRascalMCES.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdRascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRascalMCES.so CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o ../../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /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.1.2025.03.1 /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 +[ 75%] Built target testPBF +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testAUTOCORR3D.dir/link.d CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 75%] Built target rdRascalMCES +[ 75%] Built target testAUTOCORR3D [ 76%] Linking CXX executable testRDFcustom cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDFcustom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testRDFcustom.dir/link.d CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -o testRDFcustom ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' [ 76%] Built target testRDFcustom -[ 76%] Linking CXX executable test3D -cd /build/reproducible-path/rdkit-202503.1/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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/test3D.dir/link.d CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 76%] Built target test3D -[ 76%] Linking CXX executable determineBondsCatchTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DetermineBonds && /usr/bin/cmake -E cmake_link_script CMakeFiles/determineBondsCatchTest.dir/link.txt --verbose=1 -[ 77%] Linking CXX executable testMolEnumerator -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/determineBondsCatchTest.dir/link.d CMakeFiles/determineBondsCatchTest.dir/catch_tests.cpp.o -o determineBondsCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDetermineBonds.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitDistGeomHelpers.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitDistGeometry.so.1.2025.03.1 ../../../lib/libRDKitForceFieldHelpers.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitForceField.so.1.2025.03.1 ../../../lib/libRDKitOptimizer.so.1.2025.03.1 ../../../lib/libRDKitTrajectory.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 76%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRascalMCES.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdRascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRascalMCES.so CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o ../../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 77%] Built target determineBondsCatchTest -[ 77%] Linking CXX executable moldraw2DRxnTest1 -[ 77%] Built target testMolEnumerator -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 -[ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so +[ 76%] Built target rdRascalMCES +[ 76%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/moldraw2DRxnTest1.dir/link.d CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 77%] Built target moldraw2DRxnTest1 -[ 77%] Linking CXX executable molStandardizeSmallTest -cd /build/reproducible-path/rdkit-202503.1/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++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdFMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 77%] Built target rdFMCS -[ 77%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so +[ 76%] Built target rdFMCS +[ 76%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 77%] Built target molStandardizeSmallTest -[ 78%] Linking CXX executable descriptorsTestCatch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2025.03.1 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 78%] Built target MarvinParser +[ 76%] Built target MarvinParser make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend -make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build make[4]: Entering 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CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -o testRascalMCES ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 80%] Built target O3AAlign -[ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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/usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2025.03.1 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so [ 81%] Built target testRascalMCES -[ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Mol.cpp.o -MF CMakeFiles/rdchem.dir/Mol.cpp.o.d -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Mol.cpp -[ 81%] Linking CXX executable molChargeTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 81%] Built target molChargeTest -[ 82%] Linking CXX executable molFragmentTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 -[ 83%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o +[ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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 +[ 82%] Built target O3AAlign +[ 82%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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 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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-202503.1/obj-x86_64-linux-gnu' +[ 82%] Built target molChargeTest +[ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS 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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-202503.1/obj-x86_64-linux-gnu' +[ 83%] Built target molFragmentTest +[ 83%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Node.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Node.cpp [ 83%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script 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Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/MonomerInfo.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 83%] Built target TautomerQuery -[ 83%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -MF CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o.d -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp +[ 83%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Edge.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Edge.cpp [ 84%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/ScaffoldNetwork.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2025.03.1 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2025.03.1 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 84%] Built target ScaffoldNetwork -[ 84%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Node.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Node.cpp -[ 84%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Edge.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Edge.cpp -[ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Wrap/MolBundle.cpp -[ 84%] Linking CXX executable molStandardizeTest -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 [ 84%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/CIPLabeler/Sort.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 84%] Built target molStandardizeTest -[ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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 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/usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/SDMolSupplier.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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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-DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SmilesWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/SmilesWriter.cpp +[ 84%] Linking CXX executable molStandardizeTest +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp -[ 84%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 -[ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -cd 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../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /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.1.2025.03.1 /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/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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-DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/TDTMolSupplier.cpp.o -MF 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-I/build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Chirality.cpp.o -MF CMakeFiles/rdchem.dir/Chirality.cpp.o.d -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/Chirality.cpp -make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/depend -make[4]: Entering directory 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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-202503.1/obj-x86_64-linux-gnu' -[ 86%] Built target molTautomerTest -[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/Wrap/SmilesMolSupplier.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong 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CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/SubstanceGroup.cpp +[ 87%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rules/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules/Rule2.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, @@ -6792,8 +6813,6 @@ /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 88%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/RGroupDecompParams.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: /usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] @@ -6813,86 +6832,83 @@ /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 87%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o +cd 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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-202503.1/obj-x86_64-linux-gnu' -[ 92%] Built target tautomerQueryTestCatch -[ 92%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/GeneralizedSubstruct.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/GeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGeneralizedSubstruct.so.1 -o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1 ../../../lib/libRDKitGeneralizedSubstruct.so -[ 92%] Linking CXX executable testCIPLabeler -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCIPLabeler.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 92%] Built target GeneralizedSubstruct +[ 91%] Built target GeneralizedSubstruct make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/depend make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/depend make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/depend +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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/DependInfo.cmake "--color=" -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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' @@ -6902,91 +6918,104 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/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/PgSQL/rdkit/CMakeFiles/rdkit.dir/build.make Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/build.make 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92%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SynthonSpaceSearch_details.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.cpp +[ 92%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o +[ 92%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/SubstructLibrary/PatternFactory.cpp +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SynthonSpace.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -c 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/SubstructLibrary/PatternFactory.cpp -[ 94%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o +[ 93%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.cpp +[ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o cd /build/reproducible-path/rdkit-202503.1/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 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Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-202503.1/Code/PgSQL/rdkit/guc.c +[ 93%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o cd /build/reproducible-path/rdkit-202503.1/obj-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 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-DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.cpp -[ 94%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o -cd 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-I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -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-202503.1/Code/PgSQL/rdkit/rdkit_gist.c -cd /build/reproducible-path/rdkit-202503.1/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 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94%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o -[ 95%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_gist.c.o -cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2025.03.1\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code 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Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o +[ 93%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code 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CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 -[ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testCIPLabeler.dir/link.d CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o CMakeFiles/testCIPLabeler.dir/Node.cpp.o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o 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.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdMolDescriptors.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' +[ 95%] Built target testCIPLabeler +[ 95%] Built target rdMolDescriptors /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 /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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 95%] Built target rdMolDraw2D -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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 +[ 95%] Linking CXX executable tautomerQueryTestCatch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/tautomerQueryTestCatch.dir/link.d CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 95%] Built target rdTautomerQuery -[ 95%] Linking CXX executable testScaffoldNetwork -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 +[ 95%] Built target tautomerQueryTestCatch /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp: In function 'void* makeAvalonBFP(CROMol, bool, unsigned int)': /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp:1636:38: warning: unused parameter 'data' [-Wunused-parameter] 1636 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, @@ -6997,11 +7026,13 @@ /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/adapter.cpp:1637:44: warning: unused parameter 'bitFlags' [-Wunused-parameter] 1637 | unsigned int bitFlags) { | ~~~~~~~~~~~~~^~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testScaffoldNetwork.dir/link.d CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 95%] Built target testScaffoldNetwork +[ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 [ 95%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 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/usr/lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -[ 95%] Built target rdchem [ 95%] Linking CXX shared library librdkit.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1 -[ 95%] Linking CXX executable testRGroupDecompInternals -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolDraw2D.so.1.2025.03.1 ../../../lib/libRDKitMolHash.so.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitDescriptors.so.1.2025.03.1 ../../../lib/libRDKitPartialCharges.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/sql /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/sql -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/data /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/data -[ 95%] Built target testRGroupDecompInternals cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202503.1/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/PgSQL/rdkit/expected make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' [ 95%] Built target rdkit -[ 95%] Linking CXX executable gaExample -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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 +[ 95%] Linking CXX executable generalizedSubstructCatch +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 95%] Built target generalizedSubstructCatch +[ 95%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 -ldl /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 95%] Built target gaExample +[ 95%] Built target rdmolfiles +[ 95%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 [ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 -[ 95%] Linking CXX executable testReaction -cd /build/reproducible-path/rdkit-202503.1/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++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 95%] Built target rdChemReactions -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 95%] Built target testReaction -[ 96%] Linking CXX shared library ../../../lib/libRDKitSynthonSpaceSearch.so -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/SynthonSpaceSearch.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/SynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSynthonSpaceSearch.so.1 -o ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceRascalSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceHitSet.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SearchResults.cpp.o CMakeFiles/SynthonSpaceSearch.dir/MemoryMappedFileReader.cpp.o ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1 ../../../lib/libRDKitSynthonSpaceSearch.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 96%] 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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/DependInfo.cmake "--color=" +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 96%] Building CXX object Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -MF CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o.d -o CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -c /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/Wrap/rdSynthonSpaceSearch.cpp -[ 96%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so +[ 95%] Built target rdchem +[ 95%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 -[ 96%] Linking CXX executable rgroupCatchTests -cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so +[ 95%] Linking CXX executable testRGroupDecompInternals +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -[ 96%] Built target SubstructLibrary -make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/depend -make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/depend +[ 95%] Built target SubstructLibrary 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-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +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-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make 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'/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 95%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code 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/build/reproducible-path/rdkit-202503.1/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_BUILD_XYZ2MOL_SUPPORT -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-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 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-I/build/reproducible-path/rdkit-202503.1/External -I/build/reproducible-path/rdkit-202503.1/Code -I/build/reproducible-path/rdkit-202503.1/External/boost-numeric-bindings -I/usr/lib/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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-202503.1/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp +/usr/bin/c++ -g -O2 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../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1 ../../../lib/libRDKitSynthonSpaceSearch.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +[ 97%] Built target SynthonSpaceSearch +make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/depend +make -f 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/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceRascalSearch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202503.1 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../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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-202503.1/obj-x86_64-linux-gnu' [ 97%] Built target rdRGroupDecomposition +[ 97%] Linking CXX executable rgroupCatchTests +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 97%] Built target rgroupCatchTests +[ 97%] Linking CXX executable testReaction +cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[ 97%] Built target testReaction [ 98%] Linking CXX executable moldraw2DTestCatch cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitCIPLabeler.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' [ 98%] Built target moldraw2DTestCatch -[ 99%] Linking CXX executable testSynthonSpaceRascalSearch -cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceRascalSearch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testSynthonSpaceRascalSearch.dir/link.d CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -o testSynthonSpaceRascalSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[ 99%] Built target testSynthonSpaceRascalSearch -[100%] Linking CXX executable substructLibraryCatchTest +[ 99%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[100%] Built target substructLibraryCatchTest +[ 99%] Built target substructLibraryCatchTest +[100%] Linking CXX executable testSynthonSpaceRascalSearch +cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceRascalSearch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/testSynthonSpaceRascalSearch.dir/link.d CMakeFiles/testSynthonSpaceRascalSearch.dir/rascal_search_catch_tests.cpp.o -o testSynthonSpaceRascalSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[100%] Built target testSynthonSpaceRascalSearch [100%] Linking CXX executable substructLibraryTest cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' [100%] Built target substructLibraryTest +[100%] Linking CXX executable testSynthonSpaceSubstructureSearch +cd /build/reproducible-path/rdkit-202503.1/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:334:(.text+0x1866): warning: the use of `tmpnam' is dangerous, better use `mkstemp' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' +[100%] Built target testSynthonSpaceSubstructureSearch [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSynthonSpaceSearch.so cd /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSynthonSpaceSearch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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/rdSynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSynthonSpaceSearch.so CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o ../../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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 @@ -7201,13 +7244,6 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitFMCS.so.1.2025.03.1 ../../../lib/libRDKitga.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' [100%] Built target testRGroupDecomp -[100%] Linking CXX executable testSynthonSpaceSubstructureSearch -cd /build/reproducible-path/rdkit-202503.1/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:334:(.text+0x1866): warning: the use of `tmpnam' is dangerous, better use `mkstemp' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2025.03.1 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../lib/libRDKitRascalMCES.so.1.2025.03.1 ../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../lib/libRDKitDataStructs.so.1.2025.03.1 ../../../lib/libRDKitRDGeneral.so.1.2025.03.1 /usr/lib/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-202503.1/obj-x86_64-linux-gnu' -[100%] Built target testSynthonSpaceSubstructureSearch [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202503.1/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-202503.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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.1.2025.03.1 ../../../../lib/libRDKitRDBoost.so.1.2025.03.1 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2025.03.1 ../../../../lib/libRDKitMolEnumerator.so.1.2025.03.1 ../../../../lib/libRDKitTautomerQuery.so.1.2025.03.1 ../../../../lib/libRDKitMolStandardize.so.1.2025.03.1 ../../../../lib/libRDKitChemReactions.so.1.2025.03.1 ../../../../lib/libRDKitFileParsers.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2025.03.1 ../../../../lib/libRDKitChemTransforms.so.1.2025.03.1 ../../../../lib/libRDKitDepictor.so.1.2025.03.1 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2025.03.1 ../../../../lib/libRDKitMolTransforms.so.1.2025.03.1 ../../../../lib/libRDKitEigenSolvers.so.1.2025.03.1 ../../../../lib/libRDKitAlignment.so.1.2025.03.1 ../../../../lib/libRDKitFingerprints.so.1.2025.03.1 ../../../../lib/libRDKitSubgraphs.so.1.2025.03.1 ../../../../lib/libRDKitSubstructMatch.so.1.2025.03.1 ../../../../lib/libRDKitGenericGroups.so.1.2025.03.1 ../../../../lib/libRDKitSmilesParse.so.1.2025.03.1 ../../../../lib/libRDKitGraphMol.so.1.2025.03.1 ../../../../lib/libRDKitRDGeometryLib.so.1.2025.03.1 ../../../../lib/libRDKitCatalogs.so.1.2025.03.1 ../../../../lib/libRDKitDataStructs.so.1.2025.03.1 /usr/lib/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.1.2025.03.1 /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 @@ -7339,77 +7375,77 @@ Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GenericGroups Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FileParsers Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Test -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SmilesParse +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TautomerCatalog Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/FragmentCatalog Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/TransformCatalog -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/AcidBaseCatalog -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/tutorial -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Fonts +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Qt +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Qt/Demo +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/libs +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Subgraphs +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Substruct +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/configs Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/rules +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Trajectory +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/data +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/MMFF +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/CrystalFF +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/UFF +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Enumerate +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/tutorial +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/GenericGroups +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/DetermineBonds -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Qt -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Qt/Demo -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Fonts -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Test +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/StructChecker -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Depictor -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemTransforms -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MarvinParse -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/SynthonSpaceSearch/data -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/GraphMol/libs Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Catalogs Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/DataStructs Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Query Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/Data +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/Cluster Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/Cluster/Murtagh -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/DataManip Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/SimDivPickers @@ -7419,12 +7455,12 @@ Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/RDBoost Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/DistGeom Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ForceField -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ForceField/UFF Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/EigenSolvers -Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/Alignment +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/Optimizer +Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Numerics/EigenSolvers Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Geometry Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/Features Searching for files in directory /build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures @@ -8447,11 +8483,6 @@ 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... @@ -8464,17 +8495,22 @@ 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... @@ -8574,6 +8610,8 @@ 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... @@ -8630,11 +8668,11 @@ 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... @@ -8693,8 +8731,6 @@ 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... @@ -8897,11 +8933,6 @@ 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... @@ -8914,17 +8945,22 @@ 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... @@ -9024,6 +9060,8 @@ 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... @@ -9080,11 +9118,11 @@ 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... @@ -9116,11 +9154,11 @@ Generating docs for file DrawShape.h... Generating docs for file DrawText.h... Generating docs for file DrawTextCairo.h... -Generating docs for file DrawTextFT.h... -Generating docs for file DrawTextFTCairo.h... -Generating docs for file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' +Generating docs for file DrawTextFT./build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:526: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202503.1/Code/GraphMol/QueryOps.h:535: warning: Found unknown command '\overloadquery' -DrawTextFTJS.h... +h... +Generating docs for file DrawTextFTCairo.h... +Generating docs for file DrawTextFTJS.h... Generating docs for file DrawTextFTSVG.h... Generating docs for file DrawTextJS.h... Generating docs for file DrawTextNotFT.h... @@ -9145,8 +9183,6 @@ 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... @@ -11317,9 +11353,9 @@ copying downloadable files... [100%] C++Examples/example16.cpp copying static files... +Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/basic.css -Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/html/_static/sphinxdoc.css copying static files: done copying extra files... @@ -12605,10 +12641,10 @@ done preparing documents... done copying assets... -copying TeX support files... Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/make.bat -Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/Makefile -Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/latexmkrc +copying TeX support files... Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/Makefile Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/latexmkjarc +Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/latexmkrc +Writing evaluated template result to /build/reproducible-path/rdkit-202503.1/Docs/Book/_build/latex/make.bat done copying assets: done processing RDKit.tex... @@ -12876,7 +12912,7 @@ resolving references... /build/reproducible-path/rdkit-202503.1/Docs/Book/GettingStartedWithContributing.md:273: WARNING: 'myst' cross-reference target not found: 'building-rdkit-for-development' [myst.xref_missing] -WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NameResolutionError(": Failed to resolve 'img.shields.io' ([Errno -3] Temporary failure in name resolution)"))] +WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NameResolutionError(": Failed to resolve 'img.shields.io' ([Errno -3] Temporary failure in name resolution)"))] processing RDKit.tex: done writing... done copying images... [ 1%] images/Cc1ccccc1.png @@ -15002,10 +15038,10 @@ find /build/reproducible-path/rdkit-202503.1 -name rdchem.so /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so PYTHONPATH=/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/:/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib:" dh_auto_test - cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 + cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 make[2]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j40 +/usr/bin/ctest --force-new-ctest-process --verbose -j42 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. @@ -15259,6 +15295,18 @@ 40: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest 40: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 40: Test timeout computed to be: 1500 +test 41 + Start 41: graphmolMemTest1 + +41: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 +41: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol +41: Test timeout computed to be: 1500 +test 42 + Start 42: resMolSupplierTest + +42: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest +42: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol +42: Test timeout computed to be: 1500 1: core 1: RDKit 2D 1: @@ -15716,41 +15764,41 @@ 1: 2 5 1 0 1: M END 1: -3: [03:35:37] Testing Github940: property dictionaries leaking memory -3: [03:35:37] done +3: [13:04:17] Testing Github940: property dictionaries leaking memory +3: [13:04:17] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect -3: static boost any:0.000292 s -3: dynamic boost any:0.000947 s -3: static RDAny:0.000136 s -3: dynamic RDAny:0.000839 s -3: static RDValue:0 s -3: dynamic RDValue:0.000161 s +3: static boost any:0.000476 s +3: dynamic boost any:0.001735 s +3: static RDAny:0.000269 s +3: dynamic RDAny:0.001722 s +3: static RDValue:2e-06 s +3: dynamic RDValue:0.000252 s 3: deleted! -3: [03:35:37] ------------------------------------- -3: [03:35:37] Testing String Pickle Roundtrips. -3: [03:35:37] done -3: [03:35:37] ------------------------------------- -3: [03:35:37] Testing conversion of vect to string. -3: [03:35:37] done -3: [03:35:37] ------------------------------------- -3: [03:35:37] Testing returning const references. -3: [03:35:37] any cast -3: [03:35:37] done: 0.000728 300000 -3: [03:35:37] copy -3: [03:35:37] done: 0.000692 300000 -3: [03:35:37] ref -3: [03:35:37] done: 0.000767 300000 -3: [03:35:37] dict -3: [03:35:37] done: 0.001596 300000 -3: [03:35:37] ref with hasVal -3: [03:35:37] done: 0.001315 300000 -3: [03:35:37] done -3: [03:35:37] ------------------------------------- -3: [03:35:37] Testing dict update. -3: [03:35:37] done +3: [13:04:17] ------------------------------------- +3: [13:04:17] Testing String Pickle Roundtrips. +3: [13:04:17] done +3: [13:04:17] ------------------------------------- +3: [13:04:17] Testing conversion of vect to string. +3: [13:04:17] done +3: [13:04:17] ------------------------------------- +3: [13:04:17] Testing returning const references. +3: [13:04:17] any cast +3: [13:04:17] done: 0.001456 300000 +3: [13:04:17] copy +3: [13:04:17] done: 0.00112 300000 +3: [13:04:17] ref +3: [13:04:17] done: 0.001184 300000 +3: [13:04:17] dict +3: [13:04:17] done: 0.002924 300000 +3: [13:04:17] ref with hasVal +3: [13:04:17] done: 0.001831 300000 +3: [13:04:17] done +3: [13:04:17] ------------------------------------- +3: [13:04:17] Testing dict update. +3: [13:04:17] done 3: deleted! 3: deleted! 3: deleted! @@ -15769,48 +15817,48 @@ 4: == unsigned int 4: == bool 4: == std::string -5: [03:35:37] +5: [13:04:17] 5: ----------------------------------------- -5: [03:35:37] Finished: testPushAndPop() -5: [03:35:37] +5: [13:04:17] Finished: testPushAndPop() +5: [13:04:17] 5: ----------------------------------------- -5: [03:35:37] +5: [13:04:17] 5: ----------------------------------------- -6: Randomness seeded to: 1524949997 +6: Randomness seeded to: 1752931635 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: -7: [03:35:37] should not be silent -7: [03:35:37] should not be silent -7: Randomness seeded to: 2605187338 -7: [03:35:37] should not be silent -7: [03:35:37] should not be silent -7: [03:35:37] should not be silent -7: [03:35:37] should not be silent -7: [03:35:37] should not be silent -7: [03:35:37] should not be silent -7: [03:35:37] should not be silent -7: [03:35:37] should not be silent +7: [13:04:17] should not be silent +7: [13:04:17] should not be silent +7: Randomness seeded to: 4203127844 +7: [13:04:17] should not be silent +7: [13:04:17] should not be silent +7: [13:04:17] should not be silent +7: [13:04:17] should not be silent +7: [13:04:17] should not be silent +7: [13:04:17] should not be silent +7: [13:04:17] should not be silent +7: [13:04:17] should not be silent 7: =============================================================================== 7: All tests passed (26 assertions in 3 test cases) 7: -8: [03:35:37] pass -8: [03:35:37] v3 4 -8: [03:35:37] v4 5 -8: [03:35:37] SPARSE ----------------------------------- -8: [03:35:37] Set 10: 0 -8: [03:35:37] Set 11: 0 -8: [03:35:37] Set 14: 0 -8: [03:35:37] Set 10: 1 -8: [03:35:37] Get 14: 1 -8: [03:35:37] Num: 20 -8: [03:35:37] NumOn: 3 -8: [03:35:37] NumOff: 17 +8: [13:04:17] pass +8: [13:04:17] v3 4 +8: [13:04:17] v4 5 +8: [13:04:17] SPARSE ----------------------------------- +8: [13:04:17] Set 10: 0 +8: [13:04:17] Set 11: 0 +8: [13:04:17] Set 14: 0 +8: [13:04:17] Set 10: 1 +8: [13:04:17] Get 14: 1 +8: [13:04:17] Num: 20 +8: [13:04:17] NumOn: 3 +8: [13:04:17] NumOff: 17 8: 10, 11, 14, -8: [03:35:37] t2[19]: 0 -8: [03:35:37] t2[14]: 1 -8: [03:35:37] t2[19]: 0 -8: [03:35:37] t2[14]: 0 +8: [13:04:17] t2[19]: 0 +8: [13:04:17] t2[14]: 1 +8: [13:04:17] t2[19]: 0 +8: [13:04:17] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -15818,20 +15866,20 @@ 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: [03:35:37] Explicit ---------------------------------- -8: [03:35:37] Set 10: 0 -8: [03:35:37] Set 11: 0 -8: [03:35:37] Set 14: 0 -8: [03:35:37] Set 10: 1 -8: [03:35:37] Get 14: 1 -8: [03:35:37] Num: 20 -8: [03:35:37] NumOn: 3 -8: [03:35:37] NumOff: 17 +8: [13:04:17] Explicit ---------------------------------- +8: [13:04:17] Set 10: 0 +8: [13:04:17] Set 11: 0 +8: [13:04:17] Set 14: 0 +8: [13:04:17] Set 10: 1 +8: [13:04:17] Get 14: 1 +8: [13:04:17] Num: 20 +8: [13:04:17] NumOn: 3 +8: [13:04:17] NumOff: 17 8: 10, 11, 14, -8: [03:35:37] t2[19]: 0 -8: [03:35:37] t2[14]: 1 -8: [03:35:37] t2[19]: 0 -8: [03:35:37] t2[14]: 0 +8: [13:04:17] t2[19]: 0 +8: [13:04:17] t2[14]: 1 +8: [13:04:17] t2[19]: 0 +8: [13:04:17] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -15839,34 +15887,34 @@ 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: [03:35:37] Done -8: [03:35:37] Test DiscreteValue Vectors 1 ---------------------------- -8: [03:35:37] Expected failure: Value out of range -8: [03:35:37] Expected failure: Value out of range -8: [03:35:37] Expected failure: Value out of range -8: [03:35:37] Expected failure: Value out of range -8: [03:35:37] Expected failure: Value out of range -8: [03:35:37] Test DiscreteValue Vectors 2 ------------------------------ -8: [03:35:37] Test DiscreteValue Vectors 3 --------------------------- -8: [03:35:37] Test DiscreteValue Operations ----------------------------- -8: [03:35:37] Test DiscreteValue Operations 2 -------------------------- -8: [03:35:37] Test SparseIntVect ------------------------------------ -8: [03:35:37] Test SparseIntVect Serialization -------------------------- -8: [03:35:37] Test BitVect Serialization ------------------------------- -8: [03:35:37] Test BitVect to FPS ------------------------------- -8: [03:35:37] Test BitVect to binary string ------------------------------- -8: [03:35:37] Test Similarity Measures BitVect ------------------------------- -8: [03:35:37] Test Similarity Measures SparseBitVect ------------------------------- -8: [03:35:37] Test BitVect with all ones ------------------------------- -8: [03:35:37] Test Explicit BitVects: Concatenation Operation ------------------------------- -8: [03:35:37] Test bitmap operations ------------------------------- -8: [03:35:37] Test bitmaps as properties ------------------------------- -8: [03:35:37] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- -8: [03:35:37] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- -8: [03:35:37] Test RealValue Vectors 2: L1Norm ------------------------------- -8: [03:35:37] Test RealValue Vectors 3: Pickles ------------------------------- -8: [03:35:37] Test RealValue Vectors 4: Vector Operations ------------------------------- -11: Randomness seeded to: 3499554285 +8: [13:04:17] Done +8: [13:04:17] Test DiscreteValue Vectors 1 ---------------------------- +8: [13:04:17] Expected failure: Value out of range +8: [13:04:17] Expected failure: Value out of range +8: [13:04:17] Expected failure: Value out of range +8: [13:04:17] Expected failure: Value out of range +8: [13:04:17] Expected failure: Value out of range +8: [13:04:17] Test DiscreteValue Vectors 2 ------------------------------ +8: [13:04:17] Test DiscreteValue Vectors 3 --------------------------- +8: [13:04:17] Test DiscreteValue Operations ----------------------------- +8: [13:04:17] Test DiscreteValue Operations 2 -------------------------- +8: [13:04:17] Test SparseIntVect ------------------------------------ +8: [13:04:17] Test SparseIntVect Serialization -------------------------- +8: [13:04:17] Test BitVect Serialization ------------------------------- +8: [13:04:17] Test BitVect to FPS ------------------------------- +8: [13:04:17] Test BitVect to binary string ------------------------------- +8: [13:04:17] Test Similarity Measures BitVect ------------------------------- +8: [13:04:17] Test Similarity Measures SparseBitVect ------------------------------- +8: [13:04:17] Test BitVect with all ones ------------------------------- +8: [13:04:17] Test Explicit BitVects: Concatenation Operation ------------------------------- +8: [13:04:17] Test bitmap operations ------------------------------- +8: [13:04:17] Test bitmaps as properties ------------------------------- +8: [13:04:17] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- +8: [13:04:17] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- +8: [13:04:17] Test RealValue Vectors 2: L1Norm ------------------------------- +8: [13:04:17] Test RealValue Vectors 3: Pickles ------------------------------- +8: [13:04:17] Test RealValue Vectors 4: Vector Operations ------------------------------- +11: Randomness seeded to: 1753643848 11: =============================================================================== 11: All tests passed (3 assertions in 1 test case) 11: @@ -15878,8 +15926,8 @@ 17: testPointOps2D 17: **************************************** 17: test12D -17: ref1: 1.359 4.14765 ref2: 2.95372 1.43118 -17: pt1: 0.346307 1.79288 pt2: 0.160162 2.08031 +17: ref1: 0.765906 0.41448 ref2: 2.19017 3.41927 +17: pt1: 3.29817 4.94155 pt2: 0.819857 2.3332 17: **************************************** 17: test23D 17: **************************************** @@ -15925,21 +15973,21 @@ 19: --------------------------------- 19: test4UniformRealValueGrid3DOps 19: -20: Randomness seeded to: 1640518357 +20: Randomness seeded to: 232953667 20: =============================================================================== 20: All tests passed (50 assertions in 5 test cases) 20: -22: [03:35:37] ----------------------------------------- -22: [03:35:37] Testing RDNumerics: vectors and matrices Code -22: [03:35:37] --------------------------------------- -22: [03:35:37] test1Vector -22: [03:35:37] --------------------------------------- -22: [03:35:37] test2Matrix -22: [03:35:37] --------------------------------------- -22: [03:35:37] test3SquareMatrix -22: [03:35:37] --------------------------------------- -22: [03:35:37] test4SymmMatrix -23: Randomness seeded to: 3787133240 +22: [13:04:18] ----------------------------------------- +22: [13:04:18] Testing RDNumerics: vectors and matrices Code +22: [13:04:18] --------------------------------------- +22: [13:04:18] test1Vector +22: [13:04:18] --------------------------------------- +22: [13:04:18] test2Matrix +22: [13:04:18] --------------------------------------- +22: [13:04:18] test3SquareMatrix +22: [13:04:18] --------------------------------------- +22: [13:04:18] test4SymmMatrix +23: Randomness seeded to: 984389539 23: =============================================================================== 23: All tests passed (76 assertions in 3 test cases) 23: @@ -16006,34 +16054,22 @@ 28: done 28: ------------------------------------- 28: Unit tests for all UFF constraint terms. - 1/238 Test #3: testDict ............................... Passed 0.08 sec - 2/238 Test #4: testRDValue ............................ Passed 0.08 sec - 3/238 Test #6: dictTestsCatch ......................... Passed 0.08 sec - 4/238 Test #7: logTestsCatch .......................... Passed 0.08 sec - 5/238 Test #8: testDataStructs ........................ Passed 0.08 sec - 6/238 Test #9: testFPB ................................ Passed 0.07 sec - 7/238 Test #10: testMultiFPB ........................... Passed 0.07 sec - 8/238 Test #11: catchDataStructs ....................... Passed 0.07 sec - 9/238 Test #17: testTransforms ......................... Passed 0.06 sec - 10/238 Test #18: testGrid ............................... Passed 0.06 sec - 11/238 Test #19: testRealValueGrid ...................... Passed 0.06 sec - 12/238 Test #20: geometryTestsCatch ..................... Passed 0.06 sec - 13/238 Test #22: testMatrices ........................... Passed 0.06 sec - 14/238 Test #23: testConrec ............................. Passed 0.05 sec - 15/238 Test #24: testAlignment .......................... Passed 0.05 sec - 16/238 Test #26: testOptimizer .......................... Passed 0.05 sec -test 41 - Start 41: graphmolMemTest1 - -41: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 -41: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol -41: Test timeout computed to be: 1500 -test 42 - Start 42: resMolSupplierTest - -42: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest -42: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol -42: Test timeout computed to be: 1500 + 1/238 Test #3: testDict ............................... Passed 0.49 sec + 2/238 Test #4: testRDValue ............................ Passed 0.47 sec + 3/238 Test #6: dictTestsCatch ......................... Passed 0.44 sec + 4/238 Test #7: logTestsCatch .......................... Passed 0.43 sec + 5/238 Test #8: testDataStructs ........................ Passed 0.42 sec + 6/238 Test #9: testFPB ................................ Passed 0.41 sec + 7/238 Test #10: testMultiFPB ........................... Passed 0.39 sec + 8/238 Test #11: catchDataStructs ....................... Passed 0.38 sec + 9/238 Test #17: testTransforms ......................... Passed 0.33 sec + 10/238 Test #18: testGrid ............................... Passed 0.32 sec + 11/238 Test #19: testRealValueGrid ...................... Passed 0.31 sec + 12/238 Test #20: geometryTestsCatch ..................... Passed 0.31 sec + 13/238 Test #22: testMatrices ........................... Passed 0.29 sec + 14/238 Test #23: testConrec ............................. Passed 0.28 sec + 15/238 Test #24: testAlignment .......................... Passed 0.27 sec + 16/238 Test #26: testOptimizer .......................... Passed 0.24 sec test 43 Start 43: molBundleTest @@ -16118,24 +16154,23 @@ 56: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/tableTestsCatch 56: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol 56: Test timeout computed to be: 1500 -28: done -28: ------------------------------------- -28: Unit tests for copying UFF ForceFields. -28: done -28: ------------------------------------- -28: Unit test for UFF butane scan. -27: Randomness seeded to: 75002461 +test 57 + Start 57: molopsTestsCatch + +57: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/molopsTestsCatch +57: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol +57: Test timeout computed to be: 1500 +test 58 + Start 58: smiTest1 + +58: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 +58: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +58: Test timeout computed to be: 1500 +27: Randomness seeded to: 1189076282 27: =============================================================================== 27: All tests passed (20 assertions in 2 test cases) 27: - 17/238 Test #27: ForceFieldsCatch ....................... Passed 0.09 sec -33: -33: -33: -33: COPY - 18/238 Test #33: graphmolcpTest ......................... Passed 0.08 sec -29: ------------------------------------- -29: Official MMFF validation suite. + 17/238 Test #27: ForceFieldsCatch ....................... Passed 0.41 sec 31: *********************************************************** 31: test1 31: *********************************************************** @@ -16147,18 +16182,25 @@ 31: 1 1 1 0 31: *********************************************************** 31: - 19/238 Test #31: testDistGeom ........................... Passed 0.08 sec -34: [03:35:37] ---------------------- Test1 -34: [03:35:37] Done! -34: [03:35:37] ---------------------- Test2 -34: [03:35:37] Done! -34: [03:35:37] ---------------------- Test3 -34: [03:35:37] Done! -34: [03:35:37] ---------------------- Test4 -34: [03:35:37] Done! -34: [03:35:37] ---------------------- Test5 -34: [03:35:37] Done! -34: [03:35:37] + 18/238 Test #31: testDistGeom ........................... Passed 0.37 sec +29: ------------------------------------- +29: Official MMFF validation suite. +33: +33: +33: +33: COPY + 19/238 Test #33: graphmolcpTest ......................... Passed 0.33 sec +34: [13:04:18] ---------------------- Test1 +34: [13:04:18] Done! +34: [13:04:18] ---------------------- Test2 +34: [13:04:18] Done! +34: [13:04:18] ---------------------- Test3 +34: [13:04:18] Done! +34: [13:04:18] ---------------------- Test4 +34: [13:04:18] Done! +34: [13:04:18] ---------------------- Test5 +34: [13:04:18] Done! +34: [13:04:18] 34: 34: **** 34: Pre-condition Violation @@ -16170,72 +16212,55 @@ 34: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 34: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 34: 2# RDKit::QueryAtom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -34: 3# 0x000055D87D9CB7EB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 4# 0x000055D87D9C90AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest -34: 5# 0x00007FCF55C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +34: 3# 0x00005608DDF557EB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 4# 0x00005608DDF530AB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 5# 0x00007FE35A233CA8 in /lib/x86_64-linux-gnu/libc.so.6 34: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -34: 7# 0x000055D87D9C9121 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +34: 7# 0x00005608DDF53121 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest 34: ---------- 34: **** 34: -34: [03:35:37] Done! -34: [03:35:37] ---------------------- Test issue 2892580 -34: [03:35:37] Done! -34: [03:35:37] ---------------------- Test github issue 53: query molecules not matching [R] -34: [03:35:37] Done! -34: [03:35:37] ---------------------- Test queries using qualifiers instead of == -34: [03:35:37] Done! -34: [03:35:37] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -34: [03:35:37] Done! -34: [03:35:37] ---------------------- Test extra atom queries -34: [03:35:37] Done! -34: [03:35:37] ---------------------- Test extra bond queries -34: [03:35:37] Done! -34: [03:35:37] ---------------------- Test num heteroatom neighbor queries -34: [03:35:37] Done! -34: [03:35:37] ---------------------- Test atom type queries -34: [03:35:37] Done! -34: [03:35:37] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -34: [03:35:37] Done! -34: [03:35:37] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -34: [03:35:37] Done! - 20/238 Test #34: graphmolqueryTest ...................... Passed 0.08 sec -36: -------------------------- -36: -------------------------- -36: C/C=C/C(C)Cl -36: [03:35:37] Conflicting single bond directions around double bond at index 2. -36: [03:35:37] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [03:35:37] Conflicting single bond directions around double bond at index 4. -36: [03:35:37] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [03:35:37] Conflicting single bond directions around double bond at index 15. -36: [03:35:37] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [03:35:37] Conflicting single bond directions around double bond at index 2. -36: [03:35:37] BondStereo set to STEREONONE and single bond directions set to NONE. -36: [03:35:37] Conflicting single bond directions around double bond at index 1. -36: [03:35:37] BondStereo set to STEREONONE and single bond directions set to NONE. -36: -------------------------------------------------- -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing String Pickle Roundtrips. -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing reading existing pickle file (v2). -38: [03:35:37] done - 21/238 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.07 sec - 22/238 Test #39: graphmolIterTest ....................... Passed 0.07 sec -40: [03:35:37] Testing the hanoi sort -40: [03:35:37] populating vectors -test 57 - Start 57: molopsTestsCatch - -57: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/molopsTestsCatch -57: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol -57: Test timeout computed to be: 1500 -test 58 - Start 58: smiTest1 - -58: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 -58: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -58: Test timeout computed to be: 1500 +34: [13:04:18] Done! +34: [13:04:18] ---------------------- Test issue 2892580 +34: [13:04:18] Done! +34: [13:04:18] ---------------------- Test github issue 53: query molecules not matching [R] +34: [13:04:18] Done! +34: [13:04:18] ---------------------- Test queries using qualifiers instead of == +34: [13:04:18] Done! +34: [13:04:18] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +34: [13:04:18] Done! +34: [13:04:18] ---------------------- Test extra atom queries +34: [13:04:18] Done! +34: [13:04:18] ---------------------- Test extra bond queries +34: [13:04:18] Done! +34: [13:04:18] ---------------------- Test num heteroatom neighbor queries +34: [13:04:18] Done! +34: [13:04:18] ---------------------- Test atom type queries +34: [13:04:18] Done! +34: [13:04:18] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +34: [13:04:18] Done! +34: [13:04:18] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +34: [13:04:18] Done! + 20/238 Test #34: graphmolqueryTest ...................... Passed 0.32 sec +35: 1 1 2 +35: 1 1 1 +35: 2 1 0.75 +35: path: 2 +35: [13:04:18] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +35: [13:04:18] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +35: [13:04:18] Explicit valence for atom # 0 B, 5, is greater than permitted +35: [13:04:18] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [13:04:18] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [13:04:18] Explicit valence for atom # 1 C, 5, is greater than permitted +35: [13:04:18] Explicit valence for atom # 1 Si, 7, is greater than permitted +37: [13:04:18] ------------------------------------- +37: [13:04:18] Testing String Pickle Roundtrips. +38: [13:04:18] done + 21/238 Test #38: graphmoltestPicklerGlobalSetting ....... Passed 0.29 sec + 22/238 Test #39: graphmolIterTest ....................... Passed 0.29 sec +40: [13:04:18] Testing the hanoi sort +40: [13:04:18] populating vectors + 23/238 Test #41: graphmolMemTest1 ....................... Passed 0.27 sec test 59 Start 59: smiTest2 @@ -16260,17 +16285,44 @@ 62: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 62: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 62: Test timeout computed to be: 1500 -35: 1 1 2 -35: 1 1 1 -35: 2 1 0.75 -35: path: 2 -35: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: [03:35:37] Explicit valence for atom # 0 B, 5, is greater than permitted -35: [03:35:37] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [03:35:37] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [03:35:37] Explicit valence for atom # 1 C, 5, is greater than permitted -35: [03:35:37] Explicit valence for atom # 1 Si, 7, is greater than permitted +test 63 + Start 63: nontetrahedralCatch + +63: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch +63: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +63: Test timeout computed to be: 1500 +test 64 + Start 64: v2smiTestCatch + +64: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch +64: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +64: Test timeout computed to be: 1500 +test 65 + Start 65: testDepictor + +65: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor +65: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor +65: Test timeout computed to be: 1500 +28: done +28: ------------------------------------- +28: Unit tests for copying UFF ForceFields. +28: done +28: ------------------------------------- +28: Unit test for UFF butane scan. +36: -------------------------- +36: -------------------------- +36: C/C=C/C(C)Cl +36: [13:04:18] Conflicting single bond directions around double bond at index 2. +36: [13:04:18] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [13:04:18] Conflicting single bond directions around double bond at index 4. +36: [13:04:18] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [13:04:18] Conflicting single bond directions around double bond at index 15. +36: [13:04:18] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [13:04:18] Conflicting single bond directions around double bond at index 2. +36: [13:04:18] BondStereo set to STEREONONE and single bond directions set to NONE. +36: [13:04:18] Conflicting single bond directions around double bond at index 1. +36: [13:04:18] BondStereo set to STEREONONE and single bond directions set to NONE. +36: -------------------------------------------------- 1: cyclosporine a 1: RDKit 2D 1: @@ -16631,40 +16683,40 @@ 1: 30 11 1 0 1: M END 1: -46: Randomness seeded to: 1347678634 -46: [03:35:37] WARNING: not removing hydrogen atom without neighbors -46: [03:35:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:35:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:35:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:35:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:35:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:35:37] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [03:35:37] Explicit valence for atom # 1 N, 6, is greater than permitted -46: [03:35:37] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [03:35:37] Explicit valence for atom # 1 N, 5, is greater than permitted -46: [03:35:37] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [03:35:37] Explicit valence for atom # 2 O, 3, is greater than permitted -46: [03:35:37] non-ring atom 2 marked aromatic -46: [03:35:37] non-ring atom 2 marked aromatic -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 1 2 3 -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 -46: [03:35:37] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [03:35:37] Explicit valence for atom # 4 F, 2, is greater than permitted -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 6 7 8 -46: [03:35:37] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [03:35:37] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [03:35:37] WARNING: not removing hydrogen atom with dummy atom neighbors -46: [03:35:37] WARNING: not removing hydrogen atom with wedged bond -46: [03:35:37] WARNING: not removing hydrogen atom without neighbors -46: [03:35:37] WARNING: not removing hydrogen atom without neighbors -46: [03:35:37] WARNING: not removing hydrogen atom without neighbors -46: [03:35:37] WARNING: not removing hydrogen atom without neighbors -46: [03:35:37] Unreasonable formal charge on atom # 0. -46: [03:35:37] +46: Randomness seeded to: 3088671623 +46: [13:04:18] WARNING: not removing hydrogen atom without neighbors +46: [13:04:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [13:04:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [13:04:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [13:04:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [13:04:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [13:04:18] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [13:04:18] Explicit valence for atom # 1 N, 6, is greater than permitted +46: [13:04:18] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [13:04:18] Explicit valence for atom # 1 N, 5, is greater than permitted +46: [13:04:18] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [13:04:18] Explicit valence for atom # 2 O, 3, is greater than permitted +46: [13:04:18] non-ring atom 2 marked aromatic +46: [13:04:18] non-ring atom 2 marked aromatic +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 1 2 3 +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 +46: [13:04:18] Explicit valence for atom # 1 O, 3, is greater than permitted +46: [13:04:18] Explicit valence for atom # 4 F, 2, is greater than permitted +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 6 7 8 +46: [13:04:18] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [13:04:18] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [13:04:18] WARNING: not removing hydrogen atom with dummy atom neighbors +46: [13:04:18] WARNING: not removing hydrogen atom with wedged bond +46: [13:04:18] WARNING: not removing hydrogen atom without neighbors +46: [13:04:18] WARNING: not removing hydrogen atom without neighbors +46: [13:04:18] WARNING: not removing hydrogen atom without neighbors +46: [13:04:18] WARNING: not removing hydrogen atom without neighbors +46: [13:04:18] Unreasonable formal charge on atom # 0. +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -16676,20 +16728,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F134DF68 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E88CF68 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -16701,20 +16753,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F134DFF2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E88CFF2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -16726,20 +16778,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F134E085 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E88D085 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -16751,20 +16803,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F134E170 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E88D170 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -16776,20 +16828,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F134E201 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E88D201 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -16801,20 +16853,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F134E29D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E88D29D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -16826,20 +16878,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F134EBB9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E88DBB9 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -16851,20 +16903,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F134E408 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E88D408 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -16876,20 +16928,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F134E4A2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E88D4A2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -16901,20 +16953,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F134EB91 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E88DB91 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -16926,20 +16978,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F134E7B8 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E88D7B8 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -16951,24 +17003,24 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F134EB6D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E88DB6D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:35:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:35:37] WARNING: not removing hydrogen atom without neighbors -46: [03:35:37] Explicit valence for atom # 1 F greater than permitted -46: [03:35:37] +46: [13:04:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [13:04:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [13:04:18] WARNING: not removing hydrogen atom without neighbors +46: [13:04:18] Explicit valence for atom # 1 F greater than permitted +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -16980,20 +17032,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F12F4F0B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E833F0B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -17005,20 +17057,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F12F4FA0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E833FA0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -17030,20 +17082,20 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F12F4C30 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E833C30 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] +46: [13:04:18] 46: 46: **** 46: Pre-condition Violation @@ -17055,77 +17107,55 @@ 46: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 46: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -46: 3# 0x00005557F12F4CC5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 4# 0x00005557F139AB3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 5# 0x00005557F139B638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 6# 0x00005557F139BA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 7# 0x00005557F136D753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 8# 0x00005557F136DA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 9# 0x00005557F12E7E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -46: 10# 0x00007FBB10433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +46: 3# 0x0000560D3E833CC5 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 4# 0x0000560D3E8D9B3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 5# 0x0000560D3E8DA638 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 6# 0x0000560D3E8DAA9A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 7# 0x0000560D3E8AC753 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 8# 0x0000560D3E8ACA3C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 9# 0x0000560D3E826E1E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 10# 0x00007FA9F4C33CA8 in /lib/x86_64-linux-gnu/libc.so.6 46: 11# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -46: 12# 0x00005557F12E7E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +46: 12# 0x0000560D3E826E61 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch 46: ---------- 46: **** 46: -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [03:35:37] Unusual charge on atom 0 number of radical electrons set to zero -46: [03:35:37] Unusual charge on atom 0 number of radical electrons set to zero -46: [03:35:37] Unusual charge on atom 0 number of radical electrons set to zero -46: [03:35:37] non-ring atom 0 marked aromatic -46: [03:35:37] non-ring atom 0 marked aromatic -46: [03:35:37] Explicit valence for atom # 1 C, 5, is greater than permitted -46: [03:35:37] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [03:35:37] Explicit valence for atom # 3 N, 4, is greater than permitted -46: [03:35:37] Explicit valence for atom # 15 C, 5, is greater than permitted -46: [03:35:37] Explicit valence for atom # 11 C, 5, is greater than permitted -46: [03:35:37] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [03:35:37] Explicit valence for atom # 9 C, 5, is greater than permitted -46: [03:35:37] Explicit valence for atom # 9 C, 6, is greater than permitted -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 7 -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 3 -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 3 7 -46: [03:35:37] Can't kekulize mol. Unkekulized atoms: 3 7 -46: [03:35:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: [03:35:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -48: Randomness seeded to: 552192077 +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [13:04:18] Unusual charge on atom 0 number of radical electrons set to zero +46: [13:04:18] Unusual charge on atom 0 number of radical electrons set to zero +46: [13:04:18] Unusual charge on atom 0 number of radical electrons set to zero +46: [13:04:18] non-ring atom 0 marked aromatic +46: [13:04:18] non-ring atom 0 marked aromatic +46: [13:04:18] Explicit valence for atom # 1 C, 5, is greater than permitted +46: [13:04:18] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [13:04:18] Explicit valence for atom # 3 N, 4, is greater than permitted +46: [13:04:18] Explicit valence for atom # 15 C, 5, is greater than permitted +46: [13:04:18] Explicit valence for atom # 11 C, 5, is greater than permitted +46: [13:04:18] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [13:04:18] Explicit valence for atom # 9 C, 5, is greater than permitted +46: [13:04:18] Explicit valence for atom # 9 C, 6, is greater than permitted +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 7 +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 3 +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 3 7 +46: [13:04:18] Can't kekulize mol. Unkekulized atoms: 3 7 +48: Randomness seeded to: 2451432334 48: =============================================================================== 48: All tests passed (136 assertions in 8 test cases) 48: -53: Randomness seeded to: 3986353523 +53: Randomness seeded to: 1737504798 53: =============================================================================== 53: All tests passed (10 assertions in 1 test case) 53: - 23/238 Test #36: graphmoltestChirality .................. Passed 0.11 sec - 24/238 Test #41: graphmolMemTest1 ....................... Passed 0.08 sec - 25/238 Test #43: molBundleTest .......................... Passed 0.08 sec - 26/238 Test #44: testSGroup ............................. Passed 0.08 sec - 27/238 Test #45: test-valgrind .......................... Passed 0.07 sec - 28/238 Test #48: graphmolSGroupCatch .................... Passed 0.07 sec - 29/238 Test #53: queryTestsCatch ........................ Passed 0.05 sec -test 63 - Start 63: nontetrahedralCatch - -63: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch -63: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -63: Test timeout computed to be: 1500 -test 64 - Start 64: v2smiTestCatch - -64: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch -64: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -64: Test timeout computed to be: 1500 -test 65 - Start 65: testDepictor - -65: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor -65: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Depictor -65: Test timeout computed to be: 1500 + 24/238 Test #36: graphmoltestChirality .................. Passed 0.42 sec + 25/238 Test #43: molBundleTest .......................... Passed 0.31 sec + 26/238 Test #44: testSGroup ............................. Passed 0.31 sec + 27/238 Test #45: test-valgrind .......................... Passed 0.29 sec + 28/238 Test #48: graphmolSGroupCatch .................... Passed 0.25 sec test 66 Start 66: depictorCatch @@ -17150,40 +17180,224 @@ 69: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 69: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 69: Test timeout computed to be: 1500 -35: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 - 30/238 Test #1: testCoordGen ........................... Passed 0.19 sec -52: Randomness seeded to: 2703803368 +test 70 + Start 70: testAtropisomers + +70: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers +70: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +70: Test timeout computed to be: 1500 + 29/238 Test #1: testCoordGen ........................... Passed 0.89 sec +46: [13:04:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: [13:04:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. + 30/238 Test #53: queryTestsCatch ........................ Passed 0.25 sec +37: [13:04:18] done +37: [13:04:18] ------------------------------------- +37: [13:04:18] Testing reading existing pickle file (v2). +52: Randomness seeded to: 3740358705 52: =============================================================================== 52: All tests passed (14 assertions in 4 test cases) 52: - 31/238 Test #52: moliteratorTestsCatch .................. Passed 0.07 sec -54: Randomness seeded to: 2545312497 -54: =============================================================================== -54: All tests passed (6 assertions in 1 test case) -54: - 32/238 Test #54: molbundleTestsCatch .................... Passed 0.07 sec -56: Randomness seeded to: 2623786909 + 31/238 Test #52: moliteratorTestsCatch .................. Passed 0.26 sec +47: Randomness seeded to: 1789233503 +47: =============================================================================== +47: All tests passed (62 assertions in 6 test cases) +47: + 32/238 Test #47: graphmolOrganometallicsCatch ........... Passed 0.33 sec +56: Randomness seeded to: 3587330208 56: =============================================================================== 56: All tests passed (7 assertions in 2 test cases) 56: - 33/238 Test #56: tableTestsCatch ........................ Passed 0.06 sec -55: Randomness seeded to: 1520057238 + 33/238 Test #56: tableTestsCatch ........................ Passed 0.20 sec +35: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 +35: [13:04:18] non-ring atom 0 marked aromatic +35: [13:04:18] non-ring atom 0 marked aromatic +35: [13:04:18] Conflicting single bond directions around double bond at index 17. +35: [13:04:18] BondStereo set to STEREONONE and single bond directions set to NONE. +35: starting ring finding +35: done +35: starting ring finding +35: done +35: starting ring finding +35: done +35: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C +35: starting sanitization +50: Randomness seeded to: 4112890591 +50: [13:04:18] unable to set wavy bonds for double bonds: 3 +50: [13:04:18] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +50: [13:04:18] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +50: [13:04:18] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +50: [13:04:18] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +49: Randomness seeded to: 1316009653 +49: =============================================================================== +49: All tests passed (292 assertions in 12 test cases) +49: + 34/238 Test #49: graphmolAdjustQueryCatch ............... Passed 0.30 sec +54: Randomness seeded to: 2807191176 +54: =============================================================================== +54: All tests passed (6 assertions in 1 test case) +54: + 35/238 Test #54: molbundleTestsCatch .................... Passed 0.24 sec +55: Randomness seeded to: 3335693861 55: =============================================================================== 55: All tests passed (45 assertions in 4 test cases) 55: - 34/238 Test #55: pickleTestsCatch ....................... Passed 0.07 sec -47: Randomness seeded to: 3533395507 -47: =============================================================================== -47: All tests passed (62 assertions in 6 test cases) -47: - 35/238 Test #47: graphmolOrganometallicsCatch ........... Passed 0.09 sec -50: Randomness seeded to: 275285888 -50: [03:35:37] unable to set wavy bonds for double bonds: 3 -50: [03:35:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -50: [03:35:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing combining molecules using pickles. + 36/238 Test #55: pickleTestsCatch ....................... Passed 0.22 sec +57: Randomness seeded to: 2025128769 +57: =============================================================================== +57: All tests passed (230 assertions in 7 test cases) +57: + 37/238 Test #57: molopsTestsCatch ....................... Passed 0.20 sec +58: [13:04:18] WARNING: not removing hydrogen atom without neighbors +58: [13:04:18] WARNING: not removing hydrogen atom without neighbors +58: [13:04:18] WARNING: not removing hydrogen atom without neighbors +58: [13:04:18] WARNING: not removing hydrogen atom without neighbors +58: [13:04:18] WARNING: not removing hydrogen atom without neighbors +58: [13:04:18] WARNING: not removing hydrogen atom without neighbors +58: [13:04:18] WARNING: not removing hydrogen atom without neighbors +58: [13:04:18] WARNING: not removing hydrogen atom without neighbors +58: [13:04:18] WARNING: not removing hydrogen atom without neighbors +58: [13:04:18] WARNING: not removing hydrogen atom without neighbors +58: [13:04:18] WARNING: not removing hydrogen atom without neighbors +58: [13:04:18] Invalid chiral specification on atom 0 +58: [13:04:18] Invalid chiral specification on atom 0 +58: [13:04:18] Invalid chiral specification on atom 0 +58: [13:04:18] Invalid chiral specification on atom 0 +58: [13:04:18] Invalid chiral specification on atom 0 +59: [13:04:18] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +59: [13:04:18] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [13:04:18] SMILES Parse Error: syntax error while parsing: - +59: [13:04:18] SMILES Parse Error: check for mistakes around position 1: +59: [13:04:18] - +59: [13:04:18] ^ +59: [13:04:18] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +59: [13:04:18] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +59: [13:04:18] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +59: [13:04:18] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +59: [13:04:18] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +59: [13:04:18] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +59: [13:04:18] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +59: [13:04:18] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +59: [13:04:18] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +59: [13:04:18] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +59: [13:04:18] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +59: [13:04:18] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 38/238 Test #59: smiTest2 ............................... Passed 0.17 sec +test 71 + Start 71: testSquiggleDoubleBonds + +71: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds +71: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +71: Test timeout computed to be: 1500 +test 72 + Start 72: testMolSupplier + +72: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +72: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +72: Test timeout computed to be: 1500 +test 73 + Start 73: testGeneralFileReader + +73: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +73: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +73: Test timeout computed to be: 1500 +test 74 + Start 74: testMultithreadedMolSupplier + +74: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier +74: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +74: Test timeout computed to be: 1500 +test 75 + Start 75: testMolWriter + +75: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter +75: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +75: Test timeout computed to be: 1500 +test 76 + Start 76: testTplParser + +76: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser +76: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +76: Test timeout computed to be: 1500 +test 77 + Start 77: testMol2ToMol + +77: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol +77: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +77: Test timeout computed to be: 1500 +test 78 + Start 78: testSequence + +78: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence +78: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +78: Test timeout computed to be: 1500 +test 79 + Start 79: testExtendedStereoParsing + +79: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing +79: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +79: Test timeout computed to be: 1500 +test 80 + Start 80: fileParsersCatchTest + +80: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +80: Test timeout computed to be: 1500 +16: ......... +16: ---------------------------------------------------------------------- +16: Ran 9 tests in 0.034s +16: +16: OK +64: Randomness seeded to: 3876447983 +64: =============================================================================== +64: All tests passed (14 assertions in 2 test cases) +64: +63: Randomness seeded to: 4033255125 +63: [13:04:18] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [13:04:18] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [13:04:18] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [13:04:18] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [13:04:18] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [13:04:18] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [13:04:18] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [13:04:18] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +63: [13:04:18] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +63: =============================================================================== +63: All tests passed (308 assertions in 9 test cases) +63: +62: Randomness seeded to: 1582852859 +62: [13:04:18] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +62: [13:04:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [13:04:18] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +62: [13:04:18] SMARTS Parse Error: unclosed ring for input: 'C1C' +62: [13:04:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [13:04:18] SMARTS Parse Error: syntax error while parsing: C)foo +62: [13:04:18] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +62: [13:04:18] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +62: [13:04:18] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +62: [13:04:18] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +14: ...... +14: ---------------------------------------------------------------------- +14: Ran 6 tests in 0.005s +14: +14: OK + 39/238 Test #64: v2smiTestCatch ......................... Passed 0.21 sec +test 81 + Start 81: testPropertyLists + +81: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists +81: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +81: Test timeout computed to be: 1500 + 40/238 Test #63: nontetrahedralCatch .................... Passed 0.24 sec +50: [13:04:18] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +50: =============================================================================== +50: All tests passed (2295 assertions in 80 test cases) +50: + 41/238 Test #50: chiralityTestsCatch .................... Passed 0.40 sec +58: [13:04:18] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +58: [13:04:18] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +37: [13:04:18] done +37: [13:04:18] ------------------------------------- +37: [13:04:18] Testing combining molecules using pickles. 37: Atoms: 37: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 37: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 @@ -17200,37 +17414,37 @@ 37: 4 4->5 order: 1 37: 5 5->6 order: 1 37: 6 6->3 order: 1 -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing Issue164: Roundtrip Pickle Failure. -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing Issue219: Pickle Failure with Conformations. -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing Issue220: Pickle problems with bond stereochemistry. -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing query serialization. -37: [03:35:37] C=[$(C=O)] -37: [03:35:37] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing radical handling in pickles. -37: [03:35:37] done -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing sf.net issue 2788233. -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing sf.net issue 3202580. +37: [13:04:18] done +37: [13:04:18] ------------------------------------- +37: [13:04:18] Testing Issue164: Roundtrip Pickle Failure. +37: [13:04:18] done +37: [13:04:18] ------------------------------------- +37: [13:04:18] Testing Issue219: Pickle Failure with Conformations. +37: [13:04:18] done +37: [13:04:18] ------------------------------------- +37: [13:04:18] Testing Issue220: Pickle problems with bond stereochemistry. +37: [13:04:18] done +37: [13:04:18] ------------------------------------- +37: [13:04:18] Testing query serialization. +37: [13:04:18] C=[$(C=O)] +37: [13:04:18] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +37: [13:04:18] done +37: [13:04:18] ------------------------------------- +37: [13:04:18] Testing radical handling in pickles. +37: [13:04:18] done +37: [13:04:18] done +37: [13:04:18] ------------------------------------- +37: [13:04:18] Testing sf.net issue 2788233. +37: [13:04:18] done +37: [13:04:18] ------------------------------------- +37: [13:04:18] Testing sf.net issue 3202580. 37: mass! 13.0034 -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing sf.net issue 3316407. -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing sf.net issue 3496759. +37: [13:04:18] done +37: [13:04:18] ------------------------------------- +37: [13:04:18] Testing sf.net issue 3316407. +37: [13:04:18] done +37: [13:04:18] ------------------------------------- +37: [13:04:18] Testing sf.net issue 3496759. 37: smi match: *C *C 37: smi match: **=* **=* 37: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O @@ -17283,6 +17497,45 @@ 37: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 37: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 37: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... +35: done +35: starting sanitization +35: done +35: starting ring finding +35: done +35: starting ring finding +35: done +35: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 +13: ...... +13: ---------------------------------------------------------------------- +13: Ran 6 tests in 0.021s +13: +13: OK +70: [13:04:18] ---- Running with POSIX locale ----- +73: [13:04:18] +73: ----------------------------------------- +73: [13:04:18] Finished: testDetermineFormat() +73: [13:04:18] ----------------------------------------- +73: +73: [13:04:18] +73: ----------------------------------------- +74: [13:04:18] +74: ----------------------------------------- +test 82 + Start 82: XYZFileParserCatchTest + +82: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest +82: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +82: Test timeout computed to be: 1500 +test 83 + Start 83: cdxmlParserCatchTest + +83: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest +83: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +83: Test timeout computed to be: 1500 +72: [13:04:18] +72: ----------------------------------------- 37: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 37: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 37: smi match: cN(=O)~O cN(=O)~O @@ -17306,6 +17559,24 @@ 37: smi match: N=CC=O N=CC=O 37: smi match: *C(C=O)C=O *C(C=O)C=O 37: smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O + 42/238 Test #14: pyRealValueVect ........................ Passed 0.87 sec +test 84 + Start 84: molfileStereoCatchTest + +84: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest +84: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +84: Test timeout computed to be: 1500 +69: *************************************** +69: *************************************** +69: [13:04:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [13:04:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +35: [13:04:18] WARNING: not removing hydrogen atom with dummy atom neighbors +35: ------------------------------- +15: ......... +15: ---------------------------------------------------------------------- +15: Ran 9 tests in 0.031s +15: +15: OK 37: smi match: O=CC=CC=O O=CC=CC=O 37: smi match: O=CN(O)C=O O=CN(O)C=O 37: smi match: O=CN(S)C=O O=CN(S)C=O @@ -17326,6 +17597,23 @@ 37: smi match: C=CCO C=CCO 37: smi match: C=CC=N C=CC=N 37: smi match: C=CC=O C=CC=O +25: ..... +25: ---------------------------------------------------------------------- +25: Ran 5 tests in 0.002s +25: +25: OK +25: Testing Alignment Wrapper code: +71: Randomness seeded to: 1805842091 +71: =============================================================================== +71: All tests passed (15 assertions in 3 test cases) +71: + 43/238 Test #71: testSquiggleDoubleBonds ................ Passed 0.14 sec +test 85 + Start 85: connectTheDotsTest + +85: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest +85: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +85: Test timeout computed to be: 1500 37: smi match: C=CC(=O)C=C C=CC(=O)C=C 37: smi match: C=CC=S C=CC=S 37: smi match: C=CC(=S)S C=CC(=S)S @@ -17354,115 +17642,6 @@ 37: smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1 37: smi match: NC=S NC=S 37: smi match: NC(N)=S NC(N)=S -13: ...... -13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.002s -13: -13: OK -49: Randomness seeded to: 3230442487 -49: =============================================================================== -49: All tests passed (292 assertions in 12 test cases) -49: -57: Randomness seeded to: 3333941820 -57: =============================================================================== -57: All tests passed (230 assertions in 7 test cases) -57: - 36/238 Test #57: molopsTestsCatch ....................... Passed 0.06 sec -58: [03:35:37] WARNING: not removing hydrogen atom without neighbors -58: [03:35:37] WARNING: not removing hydrogen atom without neighbors -58: [03:35:37] WARNING: not removing hydrogen atom without neighbors -58: [03:35:37] WARNING: not removing hydrogen atom without neighbors -58: [03:35:37] WARNING: not removing hydrogen atom without neighbors -58: [03:35:37] WARNING: not removing hydrogen atom without neighbors -58: [03:35:37] WARNING: not removing hydrogen atom without neighbors -58: [03:35:37] WARNING: not removing hydrogen atom without neighbors -58: [03:35:37] WARNING: not removing hydrogen atom without neighbors -58: [03:35:37] WARNING: not removing hydrogen atom without neighbors -58: [03:35:37] WARNING: not removing hydrogen atom without neighbors -58: [03:35:37] Invalid chiral specification on atom 0 -58: [03:35:37] Invalid chiral specification on atom 0 -58: [03:35:37] Invalid chiral specification on atom 0 -58: [03:35:37] Invalid chiral specification on atom 0 -58: [03:35:37] Invalid chiral specification on atom 0 -59: [03:35:37] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -59: [03:35:37] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [03:35:37] SMILES Parse Error: syntax error while parsing: - -59: [03:35:37] SMILES Parse Error: check for mistakes around position 1: -59: [03:35:37] - -59: [03:35:37] ^ -59: [03:35:37] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -59: [03:35:37] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -59: [03:35:37] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -59: [03:35:37] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -59: [03:35:37] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -59: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -59: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -59: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -59: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -59: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -59: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -59: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 37/238 Test #59: smiTest2 ............................... Passed 0.05 sec -test 70 - Start 70: testAtropisomers - -70: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers -70: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -70: Test timeout computed to be: 1500 -test 71 - Start 71: testSquiggleDoubleBonds - -71: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds -71: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -71: Test timeout computed to be: 1500 -test 72 - Start 72: testMolSupplier - -72: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -72: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -72: Test timeout computed to be: 1500 -test 73 - Start 73: testGeneralFileReader - -73: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -73: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -73: Test timeout computed to be: 1500 -test 74 - Start 74: testMultithreadedMolSupplier - -74: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier -74: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -74: Test timeout computed to be: 1500 -test 75 - Start 75: testMolWriter - -75: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter -75: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -75: Test timeout computed to be: 1500 -test 76 - Start 76: testTplParser - -76: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser -76: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -76: Test timeout computed to be: 1500 -test 77 - Start 77: testMol2ToMol - -77: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol -77: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -77: Test timeout computed to be: 1500 -35: [03:35:37] non-ring atom 0 marked aromatic -35: [03:35:37] non-ring atom 0 marked aromatic -35: [03:35:37] Conflicting single bond directions around double bond at index 17. -35: [03:35:37] BondStereo set to STEREONONE and single bond directions set to NONE. -35: starting ring finding -35: done -35: starting ring finding -35: done -35: starting ring finding -35: done -35: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C -35: starting sanitization 37: smi match: C=CN C=CN 37: smi match: NOC=O NOC=O 37: smi match: C1CN1 C1CN1 @@ -17473,6 +17652,17 @@ 37: smi match: *C=N *C=N 37: smi match: N=CC=O N=CC=O 37: smi match: N=CS N=CS +35: [13:04:18] Explicit valence for atom # 0 N, 4, is greater than permitted +70: [13:04:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [13:04:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [13:04:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 44/238 Test #16: pyFPB .................................. Passed 0.88 sec +test 86 + Start 86: v2MolSuppliers + +86: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers +86: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +86: Test timeout computed to be: 1500 37: smi match: N=C=N N=C=N 37: smi match: N=C=O N=C=O 37: smi match: N=C=S N=C=S @@ -17492,6 +17682,7 @@ 37: smi match: [SiH4] [SiH4] 37: smi match: NS NS 37: smi match: NCN NCN +46: [13:04:18] Explicit valence for atom # 1 O, 3, is greater than permitted 37: smi match: cC(c)(O)O cC(c)(O)O 37: smi match: *C(c)O *C(c)O 37: smi match: C=CS(c)(=O)=O C=CS(c)(=O)=O @@ -17510,6 +17701,14 @@ 37: smi match: SC(S)(S)S SC(S)(S)S 37: smi match: OS(O)(O)O OS(O)(O)O 37: smi match: O=N(=O)C[SH](=O)=O O=N(=O)C[SH](=O)=O +70: [13:04:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.094s +2: +2: OK +46: [13:04:18] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +46: [13:04:18] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 37: smi match: O=N(O)C[SH](=O)=O O=N(O)C[SH](=O)=O 37: smi match: N#CS N#CS 37: smi match: C=NO C=NO @@ -17529,10 +17728,26 @@ 37: smi match: N=CC=NO N=CC=NO 37: smi match: N#CCC#N N#CCC#N 37: smi match: CON=O CON=O -37: smi match: C=CN C=CN -37: smi match: C=N[SH](=O)=O C=N[SH](=O)=O -37: smi match: NN=O NN=O -37: smi match: NC(=O)S NC(=O)S +46: [13:04:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [13:04:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 45/238 Test #76: testTplParser .......................... Passed 0.12 sec +70: [13:04:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 87 + Start 87: v2FileParsersCatchTest + +87: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest +87: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +87: Test timeout computed to be: 1500 +73: [13:04:18] Finished: testSdf() +73: [13:04:18] ----------------------------------------- +73: +73: [13:04:18] +73: ----------------------------------------- +37: smi match: C=CN C=CN +37: smi match: C=N[SH](=O)=O C=N[SH](=O)=O +70: [13:04:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +37: smi match: NN=O NN=O +37: smi match: NC(=O)S NC(=O)S 37: smi match: N#CS N#CS 37: smi match: NC(=O)C(N)=O NC(=O)C(N)=O 37: smi match: c=N c=N @@ -17542,7 +17757,14 @@ 37: smi match: O=CNOC=O O=CNOC=O 37: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 37: smi match: ONO ONO + 46/238 Test #79: testExtendedStereoParsing .............. Passed 0.11 sec 37: smi match: ON(~O)~O ON(~O)~O +test 88 + Start 88: atropisomersCatch + +88: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/atropisomersCatch +88: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +88: Test timeout computed to be: 1500 37: smi match: OC1COC(O)C1 OC1COC(O)C1 37: smi match: OC1CCOC1O OC1CCOC1O 37: smi match: OC1CCOC(O)C1 OC1CCOC(O)C1 @@ -17559,6 +17781,29 @@ 37: smi match: *c1-c-c-ccN1 *c1-c-c-ccN1 37: smi match: *C(*)=C *C(*)=C 37: smi match: N#[NH+] N#[NH+] +35: [13:04:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +35: [13:04:18] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +35: [13:04:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +35: [13:04:18] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [13:04:18] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [13:04:18] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [13:04:18] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: [13:04:18] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +35: +68: Using new chirality perception +68: Test +68: +68: rxnStereoMarkedCrossed.mrv +68: +68: Test +68: +68: 145323811.mol +68: +68: [13:04:18] unsupported number of radical electrons 5 +46: [13:04:18] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. +46: [13:04:18] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom +46: [13:04:18] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom +46: [13:04:18] non-ring atom 0 marked aromatic 37: smi match: C#NO C#NO 37: smi match: OOO OOO 37: smi match: OO OO @@ -17577,6 +17822,12 @@ 37: smi match: *C=O *C=O 37: smi match: N=N N=N 37: smi match: SS SS +73: [13:04:18] Finished: testSmi() +73: [13:04:18] ----------------------------------------- +73: +73: [13:04:18] +73: ----------------------------------------- +69: [13:04:18] bond with order 0 found on line 7. This is not part of the MDL specification. 37: smi match: O=C1CCNC(=O)O1 O=C1CCNC(=O)O1 37: smi match: CSC(C)=N CSC(C)=N 37: smi match: COC(C)=N COC(C)=N @@ -17584,12 +17835,102 @@ 37: smi match: *C(=O)OC=O *C(=O)OC=O 37: smi match: C=CC#N C=CC#N 37: smi match: C=CC=O C=CC=O +80: Randomness seeded to: 2431221527 +80: [13:04:18] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +80: [13:04:18] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [13:04:18] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [13:04:18] SGroup 1 is invalid and will be ignored +80: [13:04:18] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +80: [13:04:18] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [13:04:18] SGroup 1 is invalid and will be ignored +80: [13:04:18] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +80: [13:04:18] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [13:04:18] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [13:04:18] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +80: [13:04:18] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [13:04:18] SGroup 1 is invalid and will be ignored +80: [13:04:18] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +80: [13:04:18] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +80: [13:04:18] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +80: [13:04:18] SGroup 1 is invalid and will be ignored +80: [13:04:18] SGroup 3 referenced on line 40 not found. +80: [13:04:18] +80: +80: **** +80: Pre-condition Violation +80: no bonds +80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp +80: Failed Expression: !d_bonds.empty() +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FA6982DA7FE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# 0x000056214BE47A99 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 16# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:18] SGroup 3 referenced on line 40 not found. +80: [13:04:18] +80: +80: **** +80: Pre-condition Violation +80: no bonds +80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp +80: Failed Expression: !d_bonds.empty() +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FA6982DA7FE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# 0x000056214BE47B42 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 16# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:18] no bonds +80: [13:04:18] SGroup 1 is invalid and will be ignored 37: smi match: CC=CC(C)=O CC=CC(C)=O 37: smi match: CC=CC(=O)OCC CC=CC(=O)OCC 37: smi match: C#CC#N C#CC#N 37: smi match: C#CC=O C#CC=O 37: smi match: C#CC(=O)OCC C#CC(=O)OCC 37: smi match: C#CC=O C#CC=O +46: [13:04:18] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [13:04:18] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +28: done + 47/238 Test #77: testMol2ToMol .......................... Passed 0.15 sec +test 89 + Start 89: multithreadedSupplierCatchTest + +89: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest +89: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +89: Test timeout computed to be: 1500 37: smi match: *C(=O)C#C *C(=O)C#C 37: smi match: C=CC=O C=CC=O 37: smi match: *C(*)(*)O *C(*)(*)O @@ -17602,458 +17943,11 @@ 37: smi match: *CC=O *CC=O 37: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O 37: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O -37: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O -37: smi match: *C[SH](=O)=O *C[SH](=O)=O -37: smi match: * * -37: smi match: *1CC1 *1CC1 -37: smi match: O=COC=O O=COC=O -37: smi match: N=C=O N=C=O -37: smi match: N=C=S N=C=S -37: smi match: O~O O~O -37: smi match: N~[SiH4] N~[SiH4] -37: smi match: *P *P -37: smi match: C=N=N C=N=N -37: smi match: *N#[NH+] *N#[NH+] -37: smi match: *S* *S* -37: smi match: ** ** -37: smi match: *CC* *CC* -37: smi match: *O[SiH3] *O[SiH3] -37: smi match: *OS(*)~O *OS(*)~O -37: smi match: N~N~O N~N~O -37: smi match: *N(~O)(~O)~O *N(~O)(~O)~O -37: smi match: *[N+](=C)[O-] *[N+](=C)[O-] -37: smi match: * * -37: smi match: *C(*)NCN(*)* *C(*)NCN(*)* -37: smi match: *OCC#N *OCC#N -37: smi match: **C=C **C=C -37: smi match: C=C[O-] C=C[O-] -37: smi match: C=CO C=CO -37: smi match: * * -37: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O -37: smi match: O=COn1ccnc1 O=COn1ccnc1 -37: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F -37: smi match: CC(C)(C)S CC(C)(C)S -37: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C -37: smi match: [CH]=O [CH]=O -37: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C -37: smi match: SS SS -37: smi match: [SH] [SH] -37: smi match: *C* *C* -37: smi match: * * -37: smi match: C[nH3+] C[nH3+] -37: smi match: cC(=N)[NH2] cC(=N)[NH2] -37: smi match: O=CN[OH] O=CN[OH] -37: smi match: NN NN -37: smi match: * * -37: smi match: *OP(=O)O* *OP(=O)O* -37: smi match: * * -37: smi match: * * -37: smi match: * * -37: smi match: *N=C(*)* *N=C(*)* -37: smi match: *C(*)(*)C=O *C(*)(*)C=O -37: smi match: CSC=O CSC=O -37: smi match: * * -58: [03:35:37] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -58: [03:35:37] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.018s -2: -2: OK -15: ......... -15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.008s -15: -15: OK -62: Randomness seeded to: 32157912 -62: [03:35:37] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -62: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -62: [03:35:37] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -62: [03:35:37] SMARTS Parse Error: unclosed ring for input: 'C1C' -62: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -62: [03:35:37] SMARTS Parse Error: syntax error while parsing: C)foo -62: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -62: [03:35:37] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -62: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -62: [03:35:37] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... -16: ......... -16: ---------------------------------------------------------------------- -16: Ran 9 tests in 0.004s -16: -16: OK - 38/238 Test #13: pyDiscreteValueVect .................... Passed 0.21 sec - 39/238 Test #49: graphmolAdjustQueryCatch ............... Passed 0.12 sec -test 78 - Start 78: testSequence - -78: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence -78: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -78: Test timeout computed to be: 1500 -test 79 - Start 79: testExtendedStereoParsing - -79: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing -79: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -79: Test timeout computed to be: 1500 -35: done -35: starting sanitization -35: done -37: smi match: O=CCl O=CCl -37: smi match: *** *** -37: smi match: *C=O *C=O -37: smi match: C[OH] C[OH] -37: smi match: C[OH] C[OH] -37: smi match: C[OH] C[OH] -37: smi match: C[OH] C[OH] -37: smi match: C[CH]=O C[CH]=O -37: smi match: *=* *=* -37: smi match: *C *C -37: smi match: C#C C#C -37: smi match: *[CH]C=C *[CH]C=C -37: smi match: cCC(=O)[OH] cCC(=O)[OH] -37: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] -37: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] -37: smi match: C=CC(=O)[OH] C=CC(=O)[OH] -37: smi match: N#CC(=O)[OH] N#CC(=O)[OH] -37: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O -37: smi match: *N(*)C*=O *N(*)C*=O -37: smi match: O=*C[OH] O=*C[OH] -37: smi match: *=C*=O *=C*=O -37: smi match: *=CC#N *=CC#N -37: smi match: *C[OH] *C[OH] -37: smi match: ** ** - 40/238 Test #2: pyCoordGen ............................. Passed 0.24 sec - 41/238 Test #15: pySparseIntVect ........................ Passed 0.22 sec -14: ...... -14: ---------------------------------------------------------------------- -14: Ran 6 tests in 0.001s -14: -14: OK -63: Randomness seeded to: 2670044943 -63: [03:35:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [03:35:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [03:35:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [03:35:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [03:35:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [03:35:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [03:35:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [03:35:37] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: Randomness seeded to: 1011720217 -64: =============================================================================== -64: All tests passed (14 assertions in 2 test cases) -64: - 42/238 Test #64: v2smiTestCatch ......................... Passed 0.06 sec -46: [03:35:37] Explicit valence for atom # 1 O, 3, is greater than permitted -46: [03:35:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [03:35:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -46: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [03:35:37] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. -46: [03:35:37] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom -46: [03:35:37] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom -46: [03:35:37] non-ring atom 0 marked aromatic -46: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -50: [03:35:37] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -50: [03:35:37] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -50: [03:35:37] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored -50: =============================================================================== -50: All tests passed (2295 assertions in 80 test cases) -50: - 43/238 Test #50: chiralityTestsCatch .................... Passed 0.13 sec -25: ..... -25: ---------------------------------------------------------------------- -25: Ran 5 tests in 0.002s -25: -25: OK -25: Testing Alignment Wrapper code: -70: [03:35:37] ---- Running with POSIX locale ----- -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [03:35:37] -72: ----------------------------------------- -73: [03:35:37] -73: ----------------------------------------- -73: [03:35:37] Finished: testDetermineFormat() -73: [03:35:37] ----------------------------------------- -73: -73: [03:35:37] -73: ----------------------------------------- -test 80 - Start 80: fileParsersCatchTest - -80: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -80: Test timeout computed to be: 1500 -test 81 - Start 81: testPropertyLists - -81: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists -81: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -81: Test timeout computed to be: 1500 -test 82 - Start 82: XYZFileParserCatchTest - -82: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest -82: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -82: Test timeout computed to be: 1500 -test 83 - Start 83: cdxmlParserCatchTest - -83: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest -83: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -83: Test timeout computed to be: 1500 -35: starting ring finding -35: done -35: starting ring finding -35: done -35: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 -35: [03:35:37] WARNING: not removing hydrogen atom with dummy atom neighbors -35: ------------------------------- -37: smi match: *C[OH] *C[OH] -37: smi match: *C(*)=O *C(*)=O -37: smi match: * * -37: smi match: *CC(=O)[OH] *CC(=O)[OH] -37: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O -37: smi match: *c *c -37: smi match: CN(C)c CN(C)c -37: smi match: c c -37: smi match: *c *c -37: smi match: *c *c -37: smi match: **:*cF **:*cF -37: smi match: cB([OH])[OH] cB([OH])[OH] -37: smi match: N~N~N N~N~N -37: smi match: *N=N* *N=N* -37: smi match: *CC[OH] *CC[OH] -37: smi match: *CC[OH] *CC[OH] -37: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] -37: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] -37: smi match: *CCC(=O)[OH] *CCC(=O)[OH] -37: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] -37: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O -37: smi match: *OC(*)=O *OC(*)=O -37: smi match: *C(=O)[OH] *C(=O)[OH] -37: smi match: O=C[OH] O=C[OH] -37: smi match: *OC(=O)O* *OC(=O)O* -37: smi match: * * -37: smi match: *OC(=O)Cl *OC(=O)Cl -37: smi match: *C#N *C#N -37: smi match: NCC(=O)NCC=O NCC(=O)NCC=O -37: smi match: SS SS -37: smi match: * * -37: smi match: *=* *=* -37: smi match: *=* *=* -37: smi match: *=* *=* -37: smi match: *=* *=* -37: smi match: C1CO1 C1CO1 -37: smi match: *OC(*)=O *OC(*)=O -37: smi match: * * -37: smi match: *O*[OH] *O*[OH] -37: smi match: COC(C)(C)O COC(C)(C)O -37: smi match: *[OH] *[OH] -37: smi match: ** ** -37: smi match: C=N[NH2] C=N[NH2] -37: smi match: C=NC=O C=NC=O -37: smi match: * * -37: smi match: C#NC C#NC -37: smi match: CN=C=O CN=C=O -37: smi match: CN=C=S CN=C=S -37: smi match: *OC(*)(*)O* *OC(*)(*)O* -37: smi match: *C(*)=O *C(*)=O -37: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C -37: smi match: *~*=O *~*=O -37: smi match: *~*=O *~*=O -63: [03:35:37] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -63: =============================================================================== -63: All tests passed (308 assertions in 9 test cases) -63: -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: *************************************** -69: *************************************** -69: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [03:35:37] bond with order 0 found on line 7. This is not part of the MDL specification. -71: Randomness seeded to: 2080959005 -71: =============================================================================== -71: All tests passed (15 assertions in 3 test cases) -71: -74: [03:35:37] -74: ----------------------------------------- -68: Using new chirality perception -68: Test -68: -68: rxnStereoMarkedCrossed.mrv -68: -68: Test -68: -68: 145323811.mol -68: -68: [03:35:37] unsupported number of radical electrons 5 -21: .................... -21: ---------------------------------------------------------------------- -21: Ran 20 tests in 0.058s -21: -21: OK -21: Testing Geometry wrapper - 44/238 Test #14: pyRealValueVect ........................ Passed 0.24 sec - 45/238 Test #16: pyFPB .................................. Passed 0.24 sec - 46/238 Test #63: nontetrahedralCatch .................... Passed 0.08 sec - 47/238 Test #71: testSquiggleDoubleBonds ................ Passed 0.06 sec -test 84 - Start 84: molfileStereoCatchTest - -84: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest -84: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -84: Test timeout computed to be: 1500 -test 85 - Start 85: connectTheDotsTest - -85: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest -85: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -85: Test timeout computed to be: 1500 -test 86 - Start 86: v2MolSuppliers - -86: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers -86: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -86: Test timeout computed to be: 1500 -test 87 - Start 87: v2FileParsersCatchTest - -87: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest -87: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -87: Test timeout computed to be: 1500 -35: [03:35:37] Explicit valence for atom # 0 N, 4, is greater than permitted -35: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [03:35:37] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -35: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -35: [03:35:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [03:35:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [03:35:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [03:35:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: [03:35:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -35: -37: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] -37: smi match: * * -37: smi match: *C#N *C#N -37: smi match: *N(=O)~O *N(=O)~O -37: smi match: N N -37: smi match: OC(=O)C(O)=O OC(=O)C(O)=O -37: smi match: C=NO C=NO -37: smi match: O~O O~O -37: smi match: c[OH] c[OH] -37: smi match: O=P(~[OH])~O O=P(~[OH])~O -37: smi match: CO~P(=O)~O CO~P(=O)~O -37: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O -37: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O -37: smi match: O=P(~O)~O O=P(~O)~O -37: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O -37: smi match: C[NH2] C[NH2] -37: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 -37: smi match: * * -37: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 -37: smi match: CS(C)~O CS(C)~O -37: smi match: CS(C)(~O)~O CS(C)(~O)~O -37: smi match: CS(N)(~O)~O CS(N)(~O)~O -37: smi match: CS([OH])(~O)~O CS([OH])(~O)~O -37: smi match: COS(C)(~O)~O COS(C)(~O)~O -37: smi match: *S(C)(~O)~O *S(C)(~O)~O -37: smi match: CN(C)C CN(C)C -37: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 -37: smi match: *C(*)=S *C(*)=S -37: smi match: *OC(*)=S *OC(*)=S -37: smi match: * * -37: smi match: C[SH] C[SH] -37: smi match: c[SH] c[SH] -37: smi match: NC(N)=S NC(N)=S -37: smi match: * * -37: smi match: ***** ***** -37: smi match: NC(N)=O NC(N)=O -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing sf.net issue 280. -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing sf.net issue 285. -37: [03:35:37] done -37: [03:35:37] done -37: [03:35:37] done -37: [03:35:37] done -37: [03:35:37] done -37: [03:35:37] done -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing Github2441: Add RDProps interface to Conformers. -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing Issue2510: Pickle Confs as double. -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing loading pickled mols with conformers -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing conformer reading/writing options -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing property reading options -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing property reading options -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing boost::serialization integration -37: [03:35:37] done -37: [03:35:37] ------------------------------------- -37: [03:35:37] Testing github issue 6036 -46: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -46: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -46: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -46: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: [03:35:37] Finished: testSdf() -73: [03:35:37] ----------------------------------------- -73: -73: [03:35:37] -73: ----------------------------------------- -73: [03:35:37] Finished: testSmi() -73: [03:35:37] ----------------------------------------- -73: -73: [03:35:37] -73: ----------------------------------------- - 48/238 Test #25: pyAlignment ............................ Passed 0.23 sec - 49/238 Test #76: testTplParser .......................... Passed 0.05 sec -72: [03:35:37] Ignoring invalid chirality label: '2_bad_chirality' -32: ...... -32: ---------------------------------------------------------------------- -32: Ran 6 tests in 0.001s -32: -32: OK -test 88 - Start 88: atropisomersCatch - -88: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/atropisomersCatch -88: Working Directory: /build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest -89: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -89: Test timeout computed to be: 1500 +81: Randomness seeded to: 1295378279 +81: =============================================================================== +81: All tests passed (95 assertions in 4 test cases) +81: +72: [13:04:18] Ignoring invalid chirality label: '2_bad_chirality' 78: Sequence: GREG 78: HELM: PEPTIDE1{G.R.E.G}$$$$ 78: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O @@ -18551,6 +18445,238 @@ 78: CONECT 163 164 164 170 78: CONECT 165 166 78: CONECT 166 167 +80: [13:04:18] SGroup line too short: 'M SBV 1 6' on line 42 +80: [13:04:18] SGroup 1 is invalid and will be ignored +80: [13:04:18] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +80: [13:04:18] SGroup 2 is invalid and will be ignored +80: [13:04:18] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_bondBookmarks.end()) +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FA6982DA68B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 8# 0x000056214BE48702 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 17# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:18] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_bondBookmarks.end()) +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FA6982DA68B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 8# 0x000056214BE487AA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 17# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:18] bookmark not found +80: [13:04:18] +80: +80: **** +80: Pre-condition Violation +80: bond is not part of the SubstanceGroup +80: Violation occurred on line 200 in file ./Code/GraphMol/SubstanceGroup.cpp +80: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 4# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FA6982DA7FE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 8# 0x000056214BE487AA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 17# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:18] bond is not part of the SubstanceGroup +80: [13:04:18] SGroup 2 is invalid and will be ignored +80: [13:04:18] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_atomBookmarks.end()) +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FA6982DA68B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 8# 0x000056214BE48B19 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 17# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:18] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_atomBookmarks.end()) +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FA6982DA68B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 8# 0x000056214BE48BC1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 17# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:18] bookmark not found +80: [13:04:18] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +80: [13:04:18] SGroup 2 is invalid and will be ignored +80: [13:04:18] WARNING: final character of V3000 array is not ')' +80: [13:04:18] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_bondBookmarks.end()) +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 9# 0x000056214BE46423 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 18# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:18] WARNING: final character of V3000 array is not ')' +80: [13:04:18] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_bondBookmarks.end()) +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 9# 0x000056214BE464BB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 18# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:18] bookmark not found +80: [13:04:18] SGroup 1 is invalid and will be ignored +80: [13:04:18] WARNING: final character of V3000 array is not ')' +80: [13:04:18] +80: +80: **** + 48/238 Test #28: testUFFForceField ...................... Passed 0.83 sec + 49/238 Test #81: testPropertyLists ...................... Passed 0.15 sec 78: CONECT 167 168 168 169 78: CONECT 170 171 78: CONECT 171 172 174 @@ -18891,6 +19017,266 @@ 78: ATOM 48 CD1 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 78: ATOM 49 CD2 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 50 N DPN A 7 0.000 0.000 0.000 1.00 0.00 N +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_atomBookmarks.end()) +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 9# 0x000056214BE46824 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 18# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:19] WARNING: final character of V3000 array is not ')' +80: [13:04:19] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_atomBookmarks.end()) +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 9# 0x000056214BE468BC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 18# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:19] bookmark not found +80: [13:04:19] SGroup 1 is invalid and will be ignored +80: [13:04:19] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_bondBookmarks.end()) +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 9# 0x000056214BE46C23 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 18# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:19] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_bondBookmarks.end()) +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 9# 0x000056214BE46CBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 18# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:19] bookmark not found +80: [13:04:19] SGroup 2 is invalid and will be ignored +80: [13:04:19] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_atomBookmarks.end()) +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 9# 0x000056214BE47022 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 18# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:19] +80: +80: **** +80: Pre-condition Violation +80: bookmark not found +80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: (lu != d_atomBookmarks.end()) +80: ---------- +80: Stacktrace: +80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 9# 0x000056214BE470BC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 18# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: ---------- +80: **** +80: +80: [13:04:19] bookmark not found +80: [13:04:19] SGroup 2 is invalid and will be ignored +80: [13:04:19] Explicit valence for atom # 2 O, 3, is greater than permitted +37: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O +37: smi match: *C[SH](=O)=O *C[SH](=O)=O +37: smi match: * * +37: smi match: *1CC1 *1CC1 +37: smi match: O=COC=O O=COC=O +37: smi match: N=C=O N=C=O +37: smi match: N=C=S N=C=S +37: smi match: O~O O~O +37: smi match: N~[SiH4] N~[SiH4] +37: smi match: *P *P +37: smi match: C=N=N C=N=N +37: smi match: *N#[NH+] *N#[NH+] +37: smi match: *S* *S* +37: smi match: ** ** +37: smi match: *CC* *CC* +37: smi match: *O[SiH3] *O[SiH3] +37: smi match: *OS(*)~O *OS(*)~O +37: smi match: N~N~O N~N~O +37: smi match: *N(~O)(~O)~O *N(~O)(~O)~O +37: smi match: *[N+](=C)[O-] *[N+](=C)[O-] +37: smi match: * * +37: smi match: *C(*)NCN(*)* *C(*)NCN(*)* +37: smi match: *OCC#N *OCC#N +37: smi match: **C=C **C=C +37: smi match: C=C[O-] C=C[O-] +37: smi match: C=CO C=CO +37: smi match: * * +37: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O +37: smi match: O=COn1ccnc1 O=COn1ccnc1 +37: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F +37: smi match: CC(C)(C)S CC(C)(C)S +37: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C +37: smi match: [CH]=O [CH]=O +37: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C +37: smi match: SS SS +37: smi match: [SH] [SH] +37: smi match: *C* *C* +37: smi match: * * +37: smi match: C[nH3+] C[nH3+] +35: [13:04:18] WARNING: not removing hydrogen atom with dummy atom neighbors +32: ...... +32: ---------------------------------------------------------------------- +32: Ran 6 tests in 0.001s +32: +32: OK +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +82: Randomness seeded to: 4126937384 +82: =============================================================================== +82: All tests passed (100 assertions in 2 test cases) +82: + 50/238 Test #82: XYZFileParserCatchTest ................. Passed 0.15 sec + 51/238 Test #13: pyDiscreteValueVect .................... Passed 1.01 sec +test 90 + Start 90: testSubstructMatch + +90: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct +90: Test timeout computed to be: 1500 +test 91 + Start 91: substructTestCatch + +91: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch +91: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct +91: Test timeout computed to be: 1500 78: HETATM 51 CA DPN A 7 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 52 C DPN A 7 0.000 0.000 0.000 1.00 0.00 C 78: HETATM 53 O DPN A 7 0.000 0.000 0.000 1.00 0.00 O @@ -19038,35 +19424,171 @@ 78: CONECT 27 28 28 29 78: END 78: -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -69: [03:35:37] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [03:35:37] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [03:35:37] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -69: generating smiles -69: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -69: converting back -69: check isomorphism -60: Randomness seeded to: 3876757242 +80: [13:04:19] Explicit valence for atom # 1 O, 3, is greater than permitted +80: [13:04:19] Explicit valence for atom # 1 C, 5, is greater than permitted +37: smi match: cC(=N)[NH2] cC(=N)[NH2] +37: smi match: O=CN[OH] O=CN[OH] +37: smi match: NN NN +37: smi match: * * +37: smi match: *OP(=O)O* *OP(=O)O* +37: smi match: * * +37: smi match: * * +37: smi match: * * +37: smi match: *N=C(*)* *N=C(*)* +37: smi match: *C(*)(*)C=O *C(*)(*)C=O +37: smi match: CSC=O CSC=O +37: smi match: * * +37: smi match: O=CCl O=CCl +37: smi match: *** *** +37: smi match: *C=O *C=O +37: smi match: C[OH] C[OH] +37: smi match: C[OH] C[OH] +37: smi match: C[OH] C[OH] +37: smi match: C[OH] C[OH] +37: smi match: C[CH]=O C[CH]=O +37: smi match: *=* *=* +37: smi match: *C *C +37: smi match: C#C C#C +37: smi match: *[CH]C=C *[CH]C=C +37: smi match: cCC(=O)[OH] cCC(=O)[OH] +37: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] +37: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] +37: smi match: C=CC(=O)[OH] C=CC(=O)[OH] +37: smi match: N#CC(=O)[OH] N#CC(=O)[OH] +37: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +test 92 + Start 92: testGenericGroups + +92: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups +92: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups +92: Test timeout computed to be: 1500 +test 93 + Start 93: testReaction + +93: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction +93: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +93: Test timeout computed to be: 1500 +46: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +85: Randomness seeded to: 2193470696 +85: =============================================================================== +85: All tests passed (8 assertions in 1 test case) +85: + 52/238 Test #25: pyAlignment ............................ Passed 0.92 sec + 53/238 Test #78: testSequence ........................... Passed 0.23 sec + 54/238 Test #85: connectTheDotsTest ..................... Passed 0.16 sec +80: [13:04:19] sanitize [13:04:19] UNK: [13:04:19] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +37: smi match: *N(*)C*=O *N(*)C*=O +37: smi match: O=*C[OH] O=*C[OH] +37: smi match: *=C*=O *=C*=O +37: smi match: *=CC#N *=CC#N +37: smi match: *C[OH] *C[OH] +37: smi match: ** ** +37: smi match: *C[OH] *C[OH] +37: smi match: *C(*)=O *C(*)=O +37: smi match: * * +37: smi match: *CC(=O)[OH] *CC(=O)[OH] +37: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O +37: smi match: *c *c +37: smi match: CN(C)c CN(C)c +37: smi match: c c +37: smi match: *c *c +37: smi match: *c *c +37: smi match: **:*cF **:*cF +37: smi match: cB([OH])[OH] cB([OH])[OH] +37: smi match: N~N~N N~N~N +70: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +70: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +test 94 + Start 94: testReactionFingerprints + +94: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints +94: Working Directory: /build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration +95: Working Directory: /build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch +96: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +96: Test timeout computed to be: 1500 +84: Randomness seeded to: 3659399737 +84: [13:04:19] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [13:04:19] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [13:04:19] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: [13:04:19] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +84: =============================================================================== +84: All tests passed (142 assertions in 6 test cases) +84: + 55/238 Test #84: molfileStereoCatchTest ................. Passed 0.20 sec +87: Randomness seeded to: 2086754302 +87: =============================================================================== +87: All tests passed (6 assertions in 1 test case) +87: + 56/238 Test #87: v2FileParsersCatchTest ................. Passed 0.15 sec +69: [13:04:19] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [13:04:19] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +69: [13:04:19] 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: 1718335981 +88: =============================================================================== +88: All tests passed (26 assertions in 2 test cases) +88: + 57/238 Test #88: atropisomersCatch ...................... Passed 0.14 sec +61: [13:04:19] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +61: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +61: [13:04:19] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +61: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +80: [13:04:19] skipping block at line 7: 'BEGIN ATOM' +37: smi match: *N=N* *N=N* +37: smi match: *CC[OH] *CC[OH] +37: smi match: *CC[OH] *CC[OH] +37: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] +37: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] +37: smi match: *CCC(=O)[OH] *CCC(=O)[OH] +37: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] +37: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O +37: smi match: *OC(*)=O *OC(*)=O +70: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 97 + Start 97: pyChemReactions + +97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" +97: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +97: Test timeout computed to be: 1500 +test 98 + Start 98: pyChemReactionEnumerations + +98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" +98: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-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-202503.1/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" +99: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +99: Test timeout computed to be: 1500 +83: Randomness seeded to: 4118411927 +83: [13:04:19] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [13:04:19] Explicit valence for atom # 3 N, 4, is greater than permitted +83: [13:04:19] CDXMLParser: failed sanitizing skipping fragment 32 +83: [13:04:19] Bad bond in CDXML skipping fragment 58... +83: [13:04:19] Invalid or missing fragment id from CDXML fragment, assigning new one... +83: [13:04:19] Bad bond in CDXML skipping fragment 58... +60: Randomness seeded to: 138175077 60: Test 60: 60: ShortAtropisomerNoCoords.cxsmi @@ -19127,75 +19649,19 @@ 60: 60: BMS-986142_atrop5.cxsmi 60: -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: Test -60: -60: BMS-986142_atrop6.cxsmi -60: -60: Test -60: -60: BMS-986142_atropBad1.cxsmi -60: -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -60: Test -60: -60: BMS-986142_atropBad2.cxsmi -60: -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -28: done - 50/238 Test #28: testUFFForceField ...................... Passed 0.25 sec - 51/238 Test #37: graphmoltestPickler .................... Passed 0.23 sec - 52/238 Test #77: testMol2ToMol .......................... Passed 0.08 sec - 53/238 Test #78: testSequence ........................... Passed 0.07 sec - 54/238 Test #79: testExtendedStereoParsing .............. Passed 0.07 sec -test 90 - Start 90: testSubstructMatch - -90: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct -90: Test timeout computed to be: 1500 -test 91 - Start 91: substructTestCatch - -91: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch -91: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct -91: Test timeout computed to be: 1500 -test 92 - Start 92: testGenericGroups - -92: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups -92: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups -92: Test timeout computed to be: 1500 -test 93 - Start 93: testReaction - -93: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction -93: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -93: Test timeout computed to be: 1500 -test 94 - Start 94: testReactionFingerprints - -94: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints -94: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -94: Test timeout computed to be: 1500 - 55/238 Test #21: testPyGeometry ......................... Passed 0.29 sec +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +46: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 68: Test 68: 68: NewChiralTest.sdf @@ -19228,796 +19694,224 @@ 68: 68: ProblemShort.mol 68: -68: [03:35:37] For a MultipleSgroup expansion, the matching orphaned bond was not found +68: [13:04:19] For a MultipleSgroup expansion, the matching orphaned bond was not found 68: The multiple sgroup will be ignored -62: [03:35:37] w block attempts to set wedging on bond 0 more than once. -62: [03:35:37] improperly formatted w block -62: [03:35:37] atom 3 is not associated with bond 1(1-2) in w block -62: [03:35:37] -62: -62: **** -62: Range Error -62: idx -62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -62: Failed Expression: 20 < 20 -62: ---------- -62: Stacktrace: -62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 7# 0x0000555D12BBD6ED in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000555D12C0E1EC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000555D12C0ECE8 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000555D12C0F14A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000555D12BE0DD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000555D12BE10BC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000555D12B7169E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x00007F6EB0033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -62: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -62: 16# 0x0000555D12B716E1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: ---------- -62: **** -62: -62: [03:35:37] -62: -62: **** -62: Range Error -62: idx -62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -62: Failed Expression: 20 < 20 -62: ---------- -62: Stacktrace: -62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 -62: 7# 0x0000555D12BBD6ED in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 8# 0x0000555D12C0E1EC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 9# 0x0000555D12C0ECE8 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 10# 0x0000555D12C0F14A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 11# 0x0000555D12BE0DD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 12# 0x0000555D12BE10BC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 13# 0x0000555D12B7169E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: 14# 0x00007F6EB0033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -62: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -62: 16# 0x0000555D12B716E1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -62: ---------- -62: **** -62: -62: [03:35:37] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [03:35:37] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -62: [03:35:37] SMARTS Parse Error: syntax error while parsing: C1C)foo -62: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' -62: [03:35:37] SMILES Parse Error: extra close parentheses while parsing: C1C)foo -62: [03:35:37] SMILES Parse Error: check for mistakes around position 4: -62: [03:35:37] C1C)foo -62: [03:35:37] ~~~^ -62: [03:35:37] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' -62: =============================================================================== -62: All tests passed (1588 assertions in 69 test cases) -62: -35: [03:35:37] WARNING: not removing hydrogen atom with dummy atom neighbors -82: Randomness seeded to: 2909591872 -82: =============================================================================== -82: All tests passed (100 assertions in 2 test cases) -82: - 56/238 Test #82: XYZFileParserCatchTest ................. Passed 0.07 sec -61: [03:35:37] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -61: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -61: [03:35:37] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -61: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -61: [03:35:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -61: [03:35:37] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged - 57/238 Test #61: smaTest1 ............................... Passed 0.17 sec -80: Randomness seeded to: 2642844844 -80: [03:35:37] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -80: [03:35:37] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [03:35:37] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [03:35:37] SGroup 1 is invalid and will be ignored -80: [03:35:37] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -80: [03:35:37] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [03:35:37] SGroup 1 is invalid and will be ignored -80: [03:35:37] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -80: [03:35:37] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [03:35:37] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [03:35:37] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -80: [03:35:37] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [03:35:37] SGroup 1 is invalid and will be ignored -80: [03:35:37] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -80: [03:35:37] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -80: [03:35:37] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -80: [03:35:37] SGroup 1 is invalid and will be ignored -80: [03:35:37] SGroup 3 referenced on line 40 not found. -80: [03:35:37] -80: -80: **** -80: Pre-condition Violation -80: no bonds -80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp -80: Failed Expression: !d_bonds.empty() -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F597AADA7FE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# 0x0000559B0D22BA99 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 16# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [03:35:37] SGroup 3 referenced on line 40 not found. -80: [03:35:37] -80: -80: **** -80: Pre-condition Violation -80: no bonds -80: Violation occurred on line 181 in file ./Code/GraphMol/SubstanceGroup.cpp -80: Failed Expression: !d_bonds.empty() -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F597AADA7FE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# 0x0000559B0D22BB42 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 16# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [03:35:37] no bonds -80: [03:35:37] SGroup 1 is invalid and will be ignored -80: [03:35:37] SGroup line too short: 'M SBV 1 6' on line 42 -80: [03:35:37] SGroup 1 is invalid and will be ignored -80: [03:35:37] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -80: [03:35:37] SGroup 2 is invalid and will be ignored -80: [03:35:37] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_bondBookmarks.end()) -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F597AADA68B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000559B0D22C702 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [03:35:37] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_bondBookmarks.end()) -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F597AADA68B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000559B0D22C7AA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [03:35:37] bookmark not found -80: [03:35:37] -80: -80: **** -80: Pre-condition Violation -80: bond is not part of the SubstanceGroup -80: Violation occurred on line 200 in file ./Code/GraphMol/SubstanceGroup.cpp -80: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 4# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F597AADA7FE in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000559B0D22C7AA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [03:35:37] bond is not part of the SubstanceGroup -80: [03:35:37] SGroup 2 is invalid and will be ignored -80: [03:35:37] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_atomBookmarks.end()) -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F597AADA68B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000559B0D22CB19 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [03:35:37] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_atomBookmarks.end()) -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F597AADA68B in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# 0x0000559B0D22CBC1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 16# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [03:35:37] bookmark not found -80: [03:35:37] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -80: [03:35:37] SGroup 2 is invalid and will be ignored -80: [03:35:37] WARNING: final character of V3000 array is not ')' -80: [03:35:37] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_bondBookmarks.end()) -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000559B0D22A423 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [03:35:37] WARNING: final character of V3000 array is not ')' -80: [03:35:37] -80: -80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_bondBookmarks.end()) -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000559B0D22A4BB in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** +86: Randomness seeded to: 1479297657 +86: [13:04:19] Ignoring invalid chirality label: '12_R_1_3_4_5' +86: [13:04:19] Ignoring invalid chirality label: '12_ANR_1_3_4_15' +86: [13:04:19] Ignoring invalid chirality label: '2_S_1_3_4' +86: [13:04:19] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' +86: =============================================================================== +86: All tests passed (24 assertions in 6 test cases) +86: + 58/238 Test #15: pySparseIntVect ........................ Passed 1.10 sec +80: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL +80: END 80: -80: [03:35:37] bookmark not found -80: [03:35:37] SGroup 1 is invalid and will be ignored -80: [03:35:37] WARNING: final character of V3000 array is not ')' -80: [03:35:37] +80: [13:04:19] 80: 80: **** 80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_atomBookmarks.end()) +80: no stream +80: Violation occurred on line 133 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp +80: Failed Expression: dp_inStream 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000559B0D22A824 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x000056214BE7B924 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x000056214BE2C3BD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 13# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:35:37] WARNING: final character of V3000 array is not ')' -80: [03:35:37] +80: [13:04:19] 80: 80: **** 80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_atomBookmarks.end()) +80: no stream +80: Violation occurred on line 187 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp +80: Failed Expression: dp_inStream 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000559B0D22A8BC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x000056214BE7B924 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x000056214BE2C598 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 13# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:35:37] bookmark not found -80: [03:35:37] SGroup 1 is invalid and will be ignored -80: [03:35:37] +80: [13:04:19] 80: 80: **** 80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_bondBookmarks.end()) +80: no stream +80: Violation occurred on line 409 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp +80: Failed Expression: dp_inStream 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000559B0D22AC23 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x000056214BE7B924 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x000056214BE2C9D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 13# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:35:37] +80: [13:04:19] 80: 80: **** 80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_bondBookmarks.end()) +80: no stream +80: Violation occurred on line 264 in file ./Code/GraphMol/FileParsers/TDTMolSupplier.cpp +80: Failed Expression: dp_inStream 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000559B0D22ACBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x000056214BE7B924 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x000056214BE2CD56 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 13# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:35:37] bookmark not found -80: [03:35:37] SGroup 2 is invalid and will be ignored -80: [03:35:37] +80: [13:04:19] 80: 80: **** 80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_atomBookmarks.end()) +80: no stream +80: Violation occurred on line 593 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +80: Failed Expression: dp_sInStream != nullptr 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000559B0D22B022 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x000056214BE7B924 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 4# 0x000056214BE2CFD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 13# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:35:37] +80: [13:04:19] Found a SCD/SED line with missing/empty SDT specification at line 21 +80: [13:04:19] Found a SCD/SED line with missing/empty SDT specification at line 20 +80: [13:04:19] BEGIN SGROUP line not found on line 14 +80: [13:04:19] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +80: [13:04:19] END SGROUP line not found on line 14 +80: [13:04:19] END SGROUP line not found on line 14 +80: [13:04:19] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +80: [13:04:19] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +80: [13:04:19] 80: 80: **** -80: Pre-condition Violation -80: bookmark not found -80: Violation occurred on line 245 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: (lu != d_atomBookmarks.end()) +80: Range Error +80: idx +80: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp +80: Failed Expression: 99 < 9 80: ---------- 80: Stacktrace: 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::SGroupParsing::ParseV3000SGroupsBlock[abi:cxx11](std::istream*, unsigned int, unsigned int, RDKit::RWMol*, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000559B0D22B0BC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +80: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 6# 0x000056214BE7B53F in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x000056214BE3D043 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +80: 16# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:35:37] bookmark not found -80: [03:35:37] SGroup 2 is invalid and will be ignored -80: [03:35:37] Explicit valence for atom # 2 O, 3, is greater than permitted -80: [03:35:37] Explicit valence for atom # 1 O, 3, is greater than permitted -80: [03:35:37] Explicit valence for atom # 1 C, 5, is greater than permitted -80: [03:35:37] sanitize [03:35:37] UNK: [03:35:37] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -85: Randomness seeded to: 795062611 -85: =============================================================================== -85: All tests passed (8 assertions in 1 test case) -85: - 58/238 Test #85: connectTheDotsTest ..................... Passed 0.06 sec - 59/238 Test #32: pyDistGeom ............................. Passed 0.27 sec -87: Randomness seeded to: 3824569385 -87: =============================================================================== -87: All tests passed (6 assertions in 1 test case) -87: - 60/238 Test #87: v2FileParsersCatchTest ................. Passed 0.05 sec -84: Randomness seeded to: 4185782454 -84: [03:35:37] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [03:35:37] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [03:35:37] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: [03:35:37] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -84: =============================================================================== -84: All tests passed (142 assertions in 6 test cases) -84: -86: Randomness seeded to: 742752060 -86: [03:35:37] Ignoring invalid chirality label: '12_R_1_3_4_5' -86: [03:35:37] Ignoring invalid chirality label: '12_ANR_1_3_4_15' -86: [03:35:37] Ignoring invalid chirality label: '2_S_1_3_4' -86: [03:35:37] Ignoring invalid chirality label: '2_ANS_1_3_4_5_2' -86: =============================================================================== -86: All tests passed (24 assertions in 6 test cases) -86: -test 95 - Start 95: testEnumeration - -95: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration -95: Working Directory: /build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch -96: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -96: Test timeout computed to be: 1500 -test 97 - Start 97: pyChemReactions - -97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" -97: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -97: Test timeout computed to be: 1500 -test 98 - Start 98: pyChemReactionEnumerations - -98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" -98: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-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-202503.1/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" -99: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -99: Test timeout computed to be: 1500 +80: [13:04:19] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +80: [13:04:19] Multiple ATTCHPT values for atom 2 on line 9 +37: smi match: *C(=O)[OH] *C(=O)[OH] +37: smi match: O=C[OH] O=C[OH] +37: smi match: *OC(=O)O* *OC(=O)O* +37: smi match: * * +37: smi match: *OC(=O)Cl *OC(=O)Cl +37: smi match: *C#N *C#N +37: smi match: NCC(=O)NCC=O NCC(=O)NCC=O +37: smi match: SS SS +37: smi match: * * +37: smi match: *=* *=* +37: smi match: *=* *=* +37: smi match: *=* *=* +37: smi match: *=* *=* +37: smi match: C1CO1 C1CO1 +37: smi match: *OC(*)=O *OC(*)=O +37: smi match: * * +37: smi match: *O*[OH] *O*[OH] +37: smi match: COC(C)(C)O COC(C)(C)O +37: smi match: *[OH] *[OH] +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 test 100 Start 100: testChemTransforms 100: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms 100: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms 100: Test timeout computed to be: 1500 -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -70: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -58: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -58: smi: ClC1CCCCC1 -58: smi: ClC1CCCCC1 -58: smi: ClC1CCCCC1Br -58: smi: c1ccccc1 -58: smi: c1ccncc1 -58: smi: c1cc[nH]c1 -58: smi: c1cc[nH]c1 -58: smi: c1cc[pH]c1 -58: [03:35:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -58: [03:35:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -83: Randomness seeded to: 2415597618 -83: [03:35:37] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [03:35:37] Explicit valence for atom # 3 N, 4, is greater than permitted -83: [03:35:37] CDXMLParser: failed sanitizing skipping fragment 32 -83: [03:35:37] Bad bond in CDXML skipping fragment 58... -83: [03:35:37] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: [03:35:37] Bad bond in CDXML skipping fragment 58... -88: Randomness seeded to: 3643250675 -88: =============================================================================== -88: All tests passed (26 assertions in 2 test cases) -88: -73: [03:35:37] Finished: testMae() -73: [03:35:37] ----------------------------------------- -73: -73: [03:35:37] -73: ----------------------------------------- -73: [03:35:37] Finished: testTdt() -73: [03:35:37] ----------------------------------------- -73: -81: Randomness seeded to: 649442030 -81: =============================================================================== -81: All tests passed (95 assertions in 4 test cases) -81: -46: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -46: [03:35:37] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [03:35:37] Explicit valence for atom # 0 Al, 6, is greater than permitted -46: [03:35:37] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [03:35:37] Explicit valence for atom # 1 Si, 6, is greater than permitted -46: [03:35:37] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [03:35:37] Explicit valence for atom # 0 P, 6, is greater than permitted -46: [03:35:37] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [03:35:37] Explicit valence for atom # 0 P, 7, is greater than permitted -46: [03:35:37] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [03:35:37] Explicit valence for atom # 1 As, 6, is greater than permitted -46: [03:35:37] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [03:35:37] Explicit valence for atom # 1 As, 7, is greater than permitted -46: [03:35:37] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [03:35:37] Explicit valence for atom # 0 Sb, 6, is greater than permitted -46: [03:35:37] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [03:35:37] Explicit valence for atom # 0 Sb, 7, is greater than permitted -46: [03:35:37] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [03:35:37] Explicit valence for atom # 1 Bi, 6, is greater than permitted -46: [03:35:37] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: [03:35:37] Explicit valence for atom # 1 Bi, 8, is greater than permitted -46: =============================================================================== -46: All tests passed (4479 assertions in 107 test cases) -46: -66: Randomness seeded to: 1424496085 -66: =============================================================================== -66: All tests passed (580 assertions in 18 test cases) -66: -72: [03:35:37] Finished: testMolSup() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testRandMolSup() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -60: Test -60: -60: JDQ443_3d.cxsmi -60: -60: Test -60: -60: JDQ443_atrop1.cxsmi -60: -60: Test -60: -60: JDQ443_atrop2.cxsmi -60: -60: Test -60: -60: JDQ443_atrop3.cxsmi -60: -60: Test -60: -60: JDQ443_atrop4.cxsmi -60: -60: Test -60: -60: JDQ443_atropBad1.cxsmi -60: -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 + 59/238 Test #86: v2MolSuppliers ......................... Passed 0.23 sec +69: generating smiles +69: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 +69: converting back +69: check isomorphism +61: [13:04:19] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +61: [13:04:19] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 90: ----------------- Test 1 90: Done 90: @@ -20042,17 +19936,27 @@ 90: ----------------- Testing serial numbers on recursive queries 90: Done 90: -90: [03:35:37] ------------------------------------- -90: [03:35:37] Test multithreading +90: [13:04:19] ------------------------------------- +90: [13:04:19] Test multithreading 90: reading molecules - 61/238 Test #46: graphmolTestsCatch ..................... Passed 0.24 sec - 62/238 Test #62: smiTestCatch ........................... Passed 0.19 sec - 63/238 Test #66: depictorCatch .......................... Passed 0.16 sec - 64/238 Test #73: testGeneralFileReader .................. Passed 0.13 sec - 65/238 Test #81: testPropertyLists ...................... Passed 0.09 sec - 66/238 Test #84: molfileStereoCatchTest ................. Passed 0.08 sec - 67/238 Test #86: v2MolSuppliers ......................... Passed 0.08 sec - 68/238 Test #88: atropisomersCatch ...................... Passed 0.07 sec + 60/238 Test #2: pyCoordGen ............................. Passed 1.26 sec +80: [13:04:19] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [13:04:19] SMARTS Parse Error: syntax error while parsing: [#6;R +80: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +80: [13:04:19] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +80: [13:04:19] Skipping empty SMARTS value for SMARTSQ. +80: [13:04:19] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +80: [13:04:19] Found a SCD/SED line with missing/empty SDT specification at line 12 +80: [13:04:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +37: smi match: ** ** +37: smi match: C=N[NH2] C=N[NH2] +37: smi match: C=NC=O C=NC=O +37: smi match: * * +37: smi match: C#NC C#NC +37: smi match: CN=C=O CN=C=O +37: smi match: CN=C=S CN=C=S +37: smi match: *OC(*)(*)O* *OC(*)(*)O* +37: smi match: *C(*)=O *C(*)=O test 101 Start 101: chemTransformsTestCatch @@ -20065,244 +19969,47 @@ 102: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch 102: Working Directory: /build/reproducible-path/rdkit-202503.1/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-202503.1/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" -103: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap -103: Test timeout computed to be: 1500 -test 104 - Start 104: testSubgraphs1 - -104: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 -104: Working Directory: /build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 -105: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -105: Test timeout computed to be: 1500 -test 106 - Start 106: subgraphsCatch - -106: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch -106: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -106: Test timeout computed to be: 1500 -test 107 - Start 107: filterCatalogTest - -107: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest -107: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog -107: Test timeout computed to be: 1500 -test 108 - Start 108: pyFilterCatalog - -108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" -108: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap -108: Test timeout computed to be: 1500 -83: [03:35:37] WARNING: not removing hydrogen atom without neighbors -83: [03:35:37] WARNING: not removing hydrogen atom without neighbors -83: [03:35:37] WARNING: not removing hydrogen atom without neighbors -83: [03:35:37] WARNING: not removing hydrogen atom without neighbors -83: [03:35:37] WARNING: not removing hydrogen atom without neighbors -83: [03:35:37] WARNING: not removing hydrogen atom without neighbors -83: [03:35:37] WARNING: not removing hydrogen atom without neighbors -83: [03:35:37] WARNING: not removing hydrogen atom without neighbors -83: [03:35:37] WARNING: not removing hydrogen atom without neighbors -83: [03:35:37] WARNING: not removing hydrogen atom without neighbors -83: [03:35:37] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. -83: [03:35:37] Incomplete atom labelling, cannot make bond -83: [03:35:37] Incomplete atom labelling, cannot make bond -80: [03:35:37] skipping block at line 7: 'BEGIN ATOM' -80: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL -80: END -80: -80: [03:35:37] -80: -80: **** -80: Pre-condition Violation -80: no stream -80: Violation occurred on line 133 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp -80: Failed Expression: dp_inStream -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000559B0D25F924 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000559B0D2103BD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [03:35:37] -80: -80: **** -80: Pre-condition Violation -80: no stream -80: Violation occurred on line 187 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp -80: Failed Expression: dp_inStream -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000559B0D25F924 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000559B0D210598 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [03:35:37] -80: -80: **** -80: Pre-condition Violation -80: no stream -80: Violation occurred on line 409 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp -80: Failed Expression: dp_inStream -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000559B0D25F924 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000559B0D2109D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [03:35:37] -80: -80: **** -80: Pre-condition Violation -80: no stream -80: Violation occurred on line 264 in file ./Code/GraphMol/FileParsers/TDTMolSupplier.cpp -80: Failed Expression: dp_inStream -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000559B0D25F924 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000559B0D210D56 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [03:35:37] -80: -80: **** -80: Pre-condition Violation -80: no stream -80: Violation occurred on line 593 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -80: Failed Expression: dp_sInStream != nullptr -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x0000559B0D25F924 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 4# 0x0000559B0D210FD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 21 -80: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 20 -80: [03:35:37] BEGIN SGROUP line not found on line 14 -80: [03:35:37] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -80: [03:35:37] END SGROUP line not found on line 14 -80: [03:35:37] END SGROUP line not found on line 14 -80: [03:35:37] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -80: [03:35:37] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -80: [03:35:37] -80: -80: **** -80: Range Error -80: idx -80: Violation occurred on line 329 in file ./Code/GraphMol/ROMol.cpp -80: Failed Expression: 99 < 9 -80: ---------- -80: Stacktrace: -80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -80: 2# RDKit::ROMol::getBondWithIdx(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -80: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 6# 0x0000559B0D25F53F in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000559B0D221043 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 -80: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 16# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: ---------- -80: **** -80: -80: [03:35:37] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -80: [03:35:37] Multiple ATTCHPT values for atom 2 on line 9 -80: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [03:35:37] SMARTS Parse Error: syntax error while parsing: [#6;R -80: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -80: [03:35:37] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -80: [03:35:37] Skipping empty SMARTS value for SMARTSQ. -80: [03:35:37] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -80: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 12 -80: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -80: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [03:35:37] WARNING: Skipping property bar because the value includes an illegal blank line -80: [03:35:37] WARNING: Skipping property baz because the value includes an illegal blank line -80: [03:35:37] WARNING: Skipping property bletch +21: .................... +21: ---------------------------------------------------------------------- +21: Ran 20 tests in 0.204s +21: +21: OK +21: Testing Geometry wrapper +62: [13:04:19] w block attempts to set wedging on bond 0 more than once. +62: [13:04:19] improperly formatted w block +62: [13:04:19] atom 3 is not associated with bond 1(1-2) in w block +60: Test +60: +60: BMS-986142_atrop6.cxsmi +60: +60: Test +60: +60: BMS-986142_atropBad1.cxsmi +60: +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +60: Test +60: +60: BMS-986142_atropBad2.cxsmi +60: +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +46: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +46: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored + 61/238 Test #61: smaTest1 ............................... Passed 0.55 sec +80: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [13:04:19] WARNING: Skipping property bar because the value includes an illegal blank line +80: [13:04:19] WARNING: Skipping property baz because the value includes an illegal blank line +80: [13:04:19] WARNING: Skipping property bletch 80: nope because the name includes a newline -80: [03:35:37] WARNING: Skipping property bletch +80: [13:04:19] WARNING: Skipping property bletch 80: nope2 because the name includes a newline -80: [03:35:37] +80: [13:04:19] 80: 80: **** 80: Post-condition Violation @@ -20314,28 +20021,53 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x00007F597AAC8511 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F597AAD3AA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F597AAD4F8D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007FA6982C8511 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FA6982D3AA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FA6982D4F8D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000559B0D1F5A2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000056214BE11A2C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:35:37] +80: [13:04:19] 80: 80: **** +37: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C +37: smi match: *~*=O *~*=O +37: smi match: *~*=O *~*=O +37: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] +37: smi match: * * +37: smi match: *C#N *C#N +37: smi match: *N(=O)~O *N(=O)~O +37: smi match: N N +37: smi match: OC(=O)C(O)=O OC(=O)C(O)=O +37: smi match: C=NO C=NO +37: smi match: O~O O~O +37: smi match: c[OH] c[OH] +37: smi match: O=P(~[OH])~O O=P(~[OH])~O +test 103 + Start 103: pyTautomerQuery + +103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" +103: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap +103: Test timeout computed to be: 1500 +94: [13:04:19] ------------------------------------- +94: [13:04:19] Test Reaction StructuralFingerprint +66: Randomness seeded to: 2313631430 +66: =============================================================================== +66: All tests passed (580 assertions in 18 test cases) +66: 80: Post-condition Violation 80: Element 'QQQ' not found 80: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h @@ -20345,26 +20077,26 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x00007F597AAC8511 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F597AAD3AA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F597AAD4F8D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007FA6982C8511 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FA6982D3AA2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FA6982D4F8D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000559B0D1F510A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000056214BE1110A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:35:37] +80: [13:04:19] 80: 80: **** 80: Post-condition Violation @@ -20376,26 +20108,26 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x00007F597AAC8511 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F597AAD1DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F597AAD214D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007FA6982C8511 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FA6982D1DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FA6982D214D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000559B0D1F59D4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000056214BE119D4 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:35:37] +80: [13:04:19] 80: 80: **** 80: Post-condition Violation @@ -20407,28 +20139,149 @@ 80: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 3# 0x00007F597AAC8511 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x00007F597AAD1DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 5# 0x00007F597AAD214D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 3# 0x00007FA6982C8511 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 4# 0x00007FA6982D1DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +80: 5# 0x00007FA6982D214D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 9# 0x0000559B0D1F5672 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 12# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 13# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 14# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 15# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 16# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 9# 0x000056214BE11672 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 12# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 14# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 15# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 16# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 17# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 18# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 18# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -80: [03:35:37] atom 3 has a negative isotope value. line: 15 -80: [03:35:37] Ignoring invalid chirality label: '2_bad_chirality' -80: [03:35:37] +80: [13:04:19] atom 3 has a negative isotope value. line: 15 +37: smi match: CO~P(=O)~O CO~P(=O)~O +37: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O +37: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O +37: smi match: O=P(~O)~O O=P(~O)~O +37: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O +37: smi match: C[NH2] C[NH2] +37: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 +37: smi match: * * +46: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +58: --C1CCC2(CC1)CCCCC2CCC1CCCC1 +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +70: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +37: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 + 62/238 Test #66: depictorCatch .......................... Passed 0.48 sec +37: smi match: CS(C)~O CS(C)~O +test 104 + Start 104: testSubgraphs1 + +104: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 +104: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +104: Test timeout computed to be: 1500 +37: smi match: CS(C)(~O)~O CS(C)(~O)~O +37: smi match: CS(N)(~O)~O CS(N)(~O)~O +37: smi match: CS([OH])(~O)~O CS([OH])(~O)~O +37: smi match: COS(C)(~O)~O COS(C)(~O)~O +37: smi match: *S(C)(~O)~O *S(C)(~O)~O +37: smi match: CN(C)C CN(C)C +37: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 +37: smi match: *C(*)=S *C(*)=S +70: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +70: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +37: smi match: *OC(*)=S *OC(*)=S + 63/238 Test #32: pyDistGeom ............................. Passed 0.96 sec +37: smi match: * * +37: smi match: C[SH] C[SH] +37: smi match: c[SH] c[SH] +test 105 + Start 105: testSubgraphs2 + +105: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 +105: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +105: Test timeout computed to be: 1500 +37: smi match: NC(N)=S NC(N)=S +37: smi match: * * +37: smi match: ***** ***** +37: smi match: NC(N)=O NC(N)=O +37: [13:04:19] done +37: [13:04:19] ------------------------------------- +37: [13:04:19] Testing sf.net issue 280. +37: [13:04:19] done +37: [13:04:19] ------------------------------------- +37: [13:04:19] Testing sf.net issue 285. +37: [13:04:19] done +37: [13:04:19] done +37: [13:04:19] done +37: [13:04:19] done +37: [13:04:19] done +37: [13:04:19] done +37: [13:04:19] done +37: [13:04:19] ------------------------------------- +37: [13:04:19] Testing Github2441: Add RDProps interface to Conformers. +37: [13:04:19] done +37: [13:04:19] ------------------------------------- +37: [13:04:19] Testing Issue2510: Pickle Confs as double. +37: [13:04:19] done +37: [13:04:19] ------------------------------------- +37: [13:04:19] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +37: [13:04:19] done +37: [13:04:19] ------------------------------------- +37: [13:04:19] Testing loading pickled mols with conformers +37: [13:04:19] done +37: [13:04:19] ------------------------------------- +37: [13:04:19] Testing conformer reading/writing options +37: [13:04:19] done +37: [13:04:19] ------------------------------------- +37: [13:04:19] Testing property reading options +37: [13:04:19] done +37: [13:04:19] ------------------------------------- +37: [13:04:19] Testing property reading options +94: [13:04:19] ------------------------------------- +94: [13:04:19] Test Reaction DifferenceFingerprint +70: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +93: smi: O=C1CNC(=O)CN1 + 64/238 Test #94: testReactionFingerprints ............... Passed 0.16 sec +37: [13:04:19] done +37: [13:04:19] ------------------------------------- +37: [13:04:19] Testing boost::serialization integration +37: [13:04:19] done +37: [13:04:19] ------------------------------------- +37: [13:04:19] Testing github issue 6036 +test 106 + Start 106: subgraphsCatch + +106: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch +106: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +106: Test timeout computed to be: 1500 +93: 1: O=C1CNC(=O)CN1 +93: 2: COOC +93: [13:04:19] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [13:04:19] 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]' +83: [13:04:19] WARNING: not removing hydrogen atom without neighbors +80: [13:04:19] Ignoring invalid chirality label: '2_bad_chirality' +80: [13:04:19] 80: 80: **** 80: Pre-condition Violation @@ -20441,173 +20294,19 @@ 80: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 80: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 80: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -80: 4# 0x0000559B0D234B55 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 5# 0x0000559B0D2A2E6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 6# 0x0000559B0D2A3968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 7# 0x0000559B0D2A3DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 8# 0x0000559B0D275AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 9# 0x0000559B0D275DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 10# 0x0000559B0D1E8F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -80: 11# 0x00007F597A033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +80: 4# 0x000056214BE50B55 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 5# 0x000056214BEBEE6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 6# 0x000056214BEBF968 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 7# 0x000056214BEBFDCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 8# 0x000056214BE91AD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 9# 0x000056214BE91DBC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 10# 0x000056214BE04F8E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 11# 0x00007FA697833CA8 in /lib/x86_64-linux-gnu/libc.so.6 80: 12# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -80: 13# 0x0000559B0D1E8FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +80: 13# 0x000056214BE04FD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 80: ---------- 80: **** 80: -30: ...[03:35:37] Molecule does not have explicit Hs. Consider calling AddHs() -94: [03:35:37] ------------------------------------- -94: [03:35:37] Test Reaction StructuralFingerprint -94: [03:35:37] ------------------------------------- -94: [03:35:37] Test Reaction DifferenceFingerprint -60: Test -60: -60: RP-6306_atrop1.cxsmi -60: -60: Test -60: -60: RP-6306_atrop2.cxsmi -60: -60: Test -60: -60: RP-6306_atrop3.cxsmi -60: -60: Test -60: -60: RP-6306_atrop4.cxsmi -60: -60: Test -60: -60: RP-6306_atrop5.cxsmi -60: -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -60: Test -60: -60: RP-6306_atrop6.cxsmi -60: -60: Test -60: -60: RP-6306_atropBad1.cxsmi -60: -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -60: Test -60: -60: RP-6306_atropBad2.cxsmi -60: -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -58: CbC(aC)aC -58: CaC(bC)aC -58: CbC(bC)aC -58: O.C -58: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O -58: [03:35:37] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -58: [03:35:37] SMILES Parse Error: check for mistakes around position 4: -58: [03:35:37] c%()ccccc%() -58: [03:35:37] ~~~^ -58: [03:35:37] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -58: [03:35:37] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -58: [03:35:37] SMILES Parse Error: check for mistakes around position 9: -58: [03:35:37] c%(100000)ccccc%(100000) -58: [03:35:37] ~~~~~~~~^ -58: [03:35:37] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -58: [03:35:37] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -58: [03:35:37] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -58: [03:35:37] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [03:35:37] SMILES Parse Error: check for mistakes around position 14: -58: [03:35:37] COc(c1)cccc1C# -58: [03:35:37] ~~~~~~~~~~~~~^ -58: [03:35:37] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [03:35:37] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [03:35:37] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [03:35:37] SMILES Parse Error: check for mistakes around position 14: -58: [03:35:37] COc(c1)cccc1C# -58: [03:35:37] ~~~~~~~~~~~~~^ -58: [03:35:37] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [03:35:37] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [03:35:37] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [03:35:37] SMILES Parse Error: check for mistakes around position 14: -58: [03:35:37] COc(c1)cccc1C# -58: [03:35:37] ~~~~~~~~~~~~~^ -58: [03:35:37] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: [03:35:37] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -58: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -58: C=c1s/c2n(c1=O)CCCCCCC\N=2 -58: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -58: [03:35:37] SMILES Parse Error: extra close parentheses while parsing: C) -58: [03:35:37] SMILES Parse Error: check for mistakes around position 2: -58: [03:35:37] C) -58: [03:35:37] ~^ -58: [03:35:37] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' -93: smi: O=C1CNC(=O)CN1 -93: 1: O=C1CNC(=O)CN1 -93: 2: COOC -93: [03:35:37] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' -93: O=C1CNC(=O)CN1 -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 4 -93: [03:35:37] atom 0 in product 0 has multiple charge specifications. -93: mass: 15.0001 -93: Oc1ccccn1 -93: Oc1ccc[nH]1 -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -70: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -90: processing -90: launch :0 -90: launch :1 -90: launch :2 -90: launch :3 -72: [03:35:37] Finished: testSmilesSup() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] ------------------------------------------------------ -72: [03:35:37] SMILES Parse Error: syntax error while parsing: fail -72: [03:35:37] SMILES Parse Error: check for mistakes around position 1: -72: [03:35:37] fail -72: [03:35:37] ^ -72: [03:35:37] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -72: [03:35:37] ERROR: Smiles parse error on line 3 -72: [03:35:37] ERROR: Cannot create molecule from : 'fail' -72: [03:35:37] ------------------------------------------------------ -72: [03:35:37] ------------------------------------------------------ -72: [03:35:37] >>> This may result in an infinite loop. It should finish almost immediately: -72: [03:35:37] <<< done. -72: [03:35:37] Finished: testSmilesSupFromText() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testSmilesWriter() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- 100: 1 smi: CC 100: 1 smi: CC 100: 2 smi: CCO[C@H](N)P @@ -20616,309 +20315,207 @@ 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 +90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +90: processing +90: launch :0 +90: launch :1 +90: launch :2 +90: launch :3 + 65/238 Test #37: graphmoltestPickler .................... Passed 0.95 sec +test 107 + Start 107: filterCatalogTest + +107: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest +107: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog +107: Test timeout computed to be: 1500 +83: [13:04:19] WARNING: not removing hydrogen atom without neighbors +83: [13:04:19] WARNING: not removing hydrogen atom without neighbors +83: [13:04:19] WARNING: not removing hydrogen atom without neighbors +93: O=C1CNC(=O)CN1 104: ----------------------- 104: Subgraph retrieval 104: Finished 104: ----------------------- 104: testSubgraphs2a -104: Finished -104: ----------------------- -104: testSubgraphs2 105: ----------------------- 105: Test1: pathToSubmol - 69/238 Test #58: smiTest1 ............................... Passed 0.24 sec - 70/238 Test #94: testReactionFingerprints ............... Passed 0.07 sec -72: [03:35:37] Finished: testSDWriter() -72: [03:35:37] ----------------------------------------- +62: [13:04:19] +62: +62: **** +62: Range Error +62: idx +62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +62: Failed Expression: 20 < 20 +62: ---------- +62: Stacktrace: +62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 7# 0x000055E1028A06ED in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x000055E1028F11EC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x000055E1028F1CE8 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x000055E1028F214A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x000055E1028C3DD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x000055E1028C40BC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x000055E10285469E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x00007F12B2E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +62: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +62: 16# 0x000055E1028546E1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: ---------- +62: **** +62: +73: [13:04:19] Finished: testMae() +73: [13:04:19] ----------------------------------------- +73: +73: [13:04:19] +73: ----------------------------------------- +73: [13:04:19] Finished: testTdt() +73: [13:04:19] ----------------------------------------- +73: +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 4 +83: [13:04:19] WARNING: not removing hydrogen atom without neighbors +83: [13:04:19] WARNING: not removing hydrogen atom without neighbors +83: [13:04:19] WARNING: not removing hydrogen atom without neighbors +83: [13:04:19] WARNING: not removing hydrogen atom without neighbors +72: [13:04:19] Finished: testMolSup() +72: [13:04:19] ----------------------------------------- 72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testSDSupplierEnding() -72: [03:35:37] ----------------------------------------- +72: [13:04:19] ----------------------------------------- + 66/238 Test #73: testGeneralFileReader .................. Passed 0.48 sec +test 108 + Start 108: pyFilterCatalog + +108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" +108: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap +108: Test timeout computed to be: 1500 +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +70: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +83: [13:04:19] WARNING: not removing hydrogen atom without neighbors +83: [13:04:19] WARNING: not removing hydrogen atom without neighbors +83: [13:04:19] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +104: Finished +104: ----------------------- +104: testSubgraphs2 +93: [13:04:19] atom 0 in product 0 has multiple charge specifications. +93: mass: 15.0001 +72: [13:04:19] Finished: testRandMolSup() +72: [13:04:19] ----------------------------------------- 72: -72: [03:35:37] ----------------------------------------- +72: [13:04:19] ----------------------------------------- +58: smi: ClC1CCCCC1 +58: smi: ClC1CCCCC1 +58: smi: ClC1CCCCC1Br +58: smi: c1ccccc1 +58: smi: c1ccncc1 +58: smi: c1cc[nH]c1 +58: smi: c1cc[nH]c1 +58: smi: c1cc[pH]c1 +70: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +93: Oc1ccccn1 +93: Oc1ccc[nH]1 +100: [13:04:19] SMARTS Parse Error: syntax error while parsing: bar +100: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' +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 +70: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +70: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +58: [13:04:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: [13:04:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. + 67/238 Test #105: testSubgraphs2 ......................... Passed 0.11 sec test 109 Start 109: testFragCatalog 109: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog 109: Test timeout computed to be: 1500 +70: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +40: [13:04:19] sorting (hanoi sort) vectors +62: [13:04:19] +62: +62: **** +62: Range Error +62: idx +62: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +62: Failed Expression: 20 < 20 +62: ---------- +62: Stacktrace: +62: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +62: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 3# RDKit::Canon::canonicalizeFragment(RDKit::ROMol&, int, std::vector >&, std::vector > const&, std::vector >&, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +62: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSmilesParse.so.1 +62: 7# 0x000055E1028A06ED in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 8# 0x000055E1028F11EC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 9# 0x000055E1028F1CE8 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 10# 0x000055E1028F214A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 11# 0x000055E1028C3DD3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 12# 0x000055E1028C40BC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 13# 0x000055E10285469E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: 14# 0x00007F12B2E33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +62: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +62: 16# 0x000055E1028546E1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +62: ---------- +62: **** +62: +62: [13:04:19] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [13:04:19] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +62: [13:04:19] SMARTS Parse Error: syntax error while parsing: C1C)foo +62: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' +62: [13:04:19] SMILES Parse Error: extra close parentheses while parsing: C1C)foo +62: [13:04:19] SMILES Parse Error: check for mistakes around position 4: +62: [13:04:19] C1C)foo +62: [13:04:19] ~~~^ +62: [13:04:19] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' +106: Randomness seeded to: 1981997322 +106: --------- + 68/238 Test #21: testPyGeometry ......................... Passed 1.25 sec test 110 Start 110: pyFragCatalog 110: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FragCatalog/Wrap/rough_test.py" 110: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 110: Test timeout computed to be: 1500 -72: [03:35:37] Finished: testSuppliersEmptyFile() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testCisTrans() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testStereoRound() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [03:35:37] Finished: testIssue226() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testTDTSupplier1() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -40: [03:35:37] sorting (hanoi sort) vectors -93: [03:35:37] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -93: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -93: [03:35:37] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [03:35:37] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -93: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -93: [03:35:37] SMARTS Parse Error: syntax error while parsing: [C:2]) -93: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -93: [03:35:37] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [03:35:37] SMILES Parse Error: check for mistakes around position 2: -93: [03:35:37] [Q:1][C:2][C:3](=[O:4])[O:5] -93: [03:35:37] ~^ -93: [03:35:37] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' -93: [03:35:37] reactant 2 has no mapped atoms. -93: [03:35:37] >> Atoms within one molecule have different RXN roles. -93: [03:35:37] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -93: [03:35:37] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -93: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -93: [03:35:37] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [03:35:37] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -93: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -93: [03:35:37] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -93: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -96: Randomness seeded to: 3479091337 -96: [03:35:37] atom 0 in product 0 has multiple charge specifications. -96: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 34 -96: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 36 -96: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 38 -96: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 40 -96: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 42 -96: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 87 -96: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 89 -96: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 91 -96: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 93 -96: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 95 -100: [03:35:37] SMARTS Parse Error: syntax error while parsing: bar -100: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -106: Randomness seeded to: 683616228 -106: --------- 106: =============================================================================== 106: All tests passed (11 assertions in 1 test case) 106: -83: [03:35:37] Incomplete atom labelling, cannot make bond - 71/238 Test #106: subgraphsCatch ......................... Passed 0.03 sec -72: [03:35:37] Finished: testTDTSupplier2() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -93: [03:35:37] reactant 0 has no mapped atoms. -93: [03:35:37] reactant 1 has no mapped atoms. -93: [03:35:37] reactant 3 has no mapped atoms. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 4 found multiple times. -93: [03:35:37] product atom-mapping number 5 found multiple times. -93: [03:35:37] product atom-mapping number 6 found multiple times. -93: [03:35:37] product atom-mapping number 7 found multiple times. -93: [03:35:37] product atom-mapping number 8 found multiple times. -93: [03:35:37] product atom-mapping number 12 found multiple times. -93: [03:35:37] product atom-mapping number 9 found multiple times. -93: [03:35:37] product atom-mapping number 10 found multiple times. -93: [03:35:37] product atom-mapping number 11 found multiple times. + 69/238 Test #106: subgraphsCatch ......................... Passed 0.12 sec test 111 Start 111: testDescriptors 111: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors 111: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 -72: [03:35:37] Finished: testTDTSupplier3() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testSDSupplierFromText() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] ERROR: Problems encountered parsing data fields -72: [03:35:37] ERROR: moving to the beginning of the next molecule -72: [03:35:37] ERROR: Problems encountered parsing data fields -72: [03:35:37] ERROR: moving to the beginning of the next molecule -72: [03:35:37] Spurious data before the first property will be ignored -72: [03:35:37] Property will be truncated after the first blank line -72: [03:35:37] Property will be truncated after the first blank line -72: [03:35:37] Property will be truncated after the first blank line -72: [03:35:37] Finished: testSDSupplierStrLax1() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] ERROR: Problems encountered parsing data fields -72: [03:35:37] ERROR: moving to the beginning of the next molecule -72: [03:35:37] Property will be truncated after the first blank line -72: [03:35:37] Finished: testSDSupplierStrLax2() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] ERROR: Problems encountered parsing data fields -72: [03:35:37] ERROR: moving to the beginning of the next molecule -72: [03:35:37] ERROR: Problems encountered parsing data fields -72: [03:35:37] ERROR: moving to the beginning of the next molecule -72: [03:35:37] Spurious data before the first property will be ignored -72: [03:35:37] Property will be truncated after the first blank line -72: [03:35:37] Property will be truncated after the first blank line -72: [03:35:37] Property will be truncated after the first blank line -72: [03:35:37] Finished: testSDSupplierFromTextStrLax1() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] ERROR: Problems encountered parsing data fields -72: [03:35:37] ERROR: moving to the beginning of the next molecule -72: [03:35:37] Property will be truncated after the first blank line -72: [03:35:37] Finished: testSDSupplierFromTextStrLax2() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testIssue265() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] ERROR: End of data field name not found -72: [03:35:37] ERROR: moving to the beginning of the next molecule -72: [03:35:37] Explicit valence for atom # 0 F, 2, is greater than permitted -72: [03:35:37] ERROR: Could not sanitize molecule ending on line 16 -72: [03:35:37] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -72: [03:35:37] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -72: [03:35:37] ERROR: moving to the beginning of the next molecule -72: [03:35:37] ERROR: Bond line too short: 'M END' on line 18 -72: [03:35:37] ERROR: moving to the beginning of the next molecule -72: [03:35:37] Finished: testSDErrorHandling() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testIssue381() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -93: [03:35:37] reactant 0 has no mapped atoms. -93: [03:35:37] reactant 1 has no mapped atoms. -93: [03:35:37] reactant 3 has no mapped atoms. -93: [03:35:37] reactant atom-mapping number 19 found multiple times. -93: [03:35:37] reactant atom-mapping number 25 found multiple times. -93: [03:35:37] reactant atom-mapping number 20 found multiple times. -93: [03:35:37] reactant atom-mapping number 21 found multiple times. -93: [03:35:37] reactant atom-mapping number 22 found multiple times. -93: [03:35:37] reactant atom-mapping number 23 found multiple times. -93: [03:35:37] reactant atom-mapping number 24 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [03:35:37] product atom-mapping number 5 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 4 found multiple times. -93: [03:35:37] product atom-mapping number 5 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 4 found multiple times. -93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [03:35:37] product atom-mapping number 5 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 4 found multiple times. -93: [03:35:37] product atom-mapping number 5 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 4 found multiple times. -93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 4 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 4 found multiple times. -93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 4 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 4 found multiple times. -93: F[C@](Cl)(Br)O[C@](F)(Cl)Br -93: [03:35:37] product atom-mapping number 4 found multiple times. -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 4 found multiple times. -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 4 found multiple times. -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 4 found multiple times. -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 4 -93: [03:35:37] product atom-mapping number 3 found multiple times. -93: [03:35:37] product atom-mapping number 2 found multiple times. -93: [03:35:37] product atom-mapping number 1 found multiple times. -93: [03:35:37] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 4 -93: [03:35:37] product atom-mapping number 6 not found in reactants. -93: [03:35:37] product atom-mapping number 7 not found in reactants. -93: [03:35:37] product atom-mapping number 8 not found in reactants. -93: [03:35:37] product atom-mapping number 7 not found in reactants. -93: [03:35:37] product atom-mapping number 8 not found in reactants. -93: [03:35:37] product atom-mapping number 9 not found in reactants. -93: [03:35:37] product atom-mapping number 10 not found in reactants. -93: [03:35:37] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 6 -93: [03:35:37] product atom-mapping number 7 not found in reactants. -93: [03:35:37] product atom-mapping number 8 not found in reactants. -93: [03:35:37] product atom-mapping number 9 not found in reactants. -93: [03:35:37] product atom-mapping number 10 not found in reactants. -93: [03:35:37] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 6 -101: Randomness seeded to: 591173444 -101: [03:35:37] Incomplete atom labelling, cannot make bond -101: [03:35:37] +101: Randomness seeded to: 2600760124 +101: [13:04:19] Incomplete atom labelling, cannot make bond +101: [13:04:19] 101: 101: **** 101: Invariant Violation @@ -20931,115 +20528,118 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/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-202503.1/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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000561C83B045D6 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000561C83B55A6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000561C83B56568 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000561C83B569CA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000561C83B28813 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000561C83B28AFC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000561C83AF882E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F1CFA233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x0000563758A465D6 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000563758A97A6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000563758A98568 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000563758A989CA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000563758A6A813 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000563758A6AAFC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000563758A3A82E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007FF651233CA8 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# 0x0000561C83AF8871 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000563758A3A871 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -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 -96: [03:35:37] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [03:35:37] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [03:35:37] SMARTS Parse Error: unclosed ring for input: 'CC1' -96: [03:35:37] SMILES Parse Error: unclosed ring for input: 'CC1' -96: [03:35:37] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [03:35:37] product atom-mapping number 2 not found in reactants. +58: CbC(aC)aC +58: CaC(bC)aC +58: CbC(bC)aC +58: O.C +93: [13:04:19] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +93: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +93: [13:04:19] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [13:04:19] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +93: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +93: [13:04:19] SMARTS Parse Error: syntax error while parsing: [C:2]) +93: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +83: [13:04:19] Incomplete atom labelling, cannot make bond +83: [13:04:19] Incomplete atom labelling, cannot make bond 60: Test 60: -60: RP-6306_3d.cxsmi +60: JDQ443_3d.cxsmi 60: 60: Test 60: -60: Sotorasib_atrop1.cxsmi +60: JDQ443_atrop1.cxsmi 60: 60: Test 60: -60: Sotorasib_atrop2.cxsmi +60: JDQ443_atrop2.cxsmi 60: 60: Test 60: -60: Sotorasib_atrop3.cxsmi +60: JDQ443_atrop3.cxsmi 60: 60: Test 60: -60: Sotorasib_atrop4.cxsmi +60: JDQ443_atrop4.cxsmi 60: 60: Test 60: -60: Sotorasib_atrop5.cxsmi +60: JDQ443_atropBad1.cxsmi 60: -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -60: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored - 72/238 Test #105: testSubgraphs2 ......................... Passed 0.04 sec -96: [03:35:37] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -83: [03:35:37] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [03:35:37] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -83: [03:35:37] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +62: =============================================================================== +62: All tests passed (1588 assertions in 69 test cases) +62: +93: [13:04:19] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [13:04:19] SMILES Parse Error: check for mistakes around position 2: +93: [13:04:19] [Q:1][C:2][C:3](=[O:4])[O:5] +93: [13:04:19] ~^ +93: [13:04:19] 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]' +96: Randomness seeded to: 2866377922 +96: [13:04:19] atom 0 in product 0 has multiple charge specifications. +58: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 + 70/238 Test #62: smiTestCatch ........................... Passed 0.74 sec test 112 Start 112: testAUTOCORR2D 112: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 112: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 -96: [03:35:37] product atom-mapping number 2 not found in reactants. -96: [03:35:37] CX Extensions: Substance group hierarchy is not always preserved. -96: [03:35:37] CX Extensions: Substance group hierarchy is not always preserved. -83: [03:35:37] Failed to parse XML fragment 5 node: b attribute: Order: 5 -83: [03:35:37] Invalid or missing fragment id from CDXML fragment, assigning new one... -83: =============================================================================== -83: All tests passed (263 assertions in 7 test cases) -83: -72: [03:35:37] Finished: testSetStreamIndices() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testMixIterAndRandom() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: build: -60: Test -60: -60: Sotorasib_atropBad1.cxsmi -60: -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -101: [03:35:37] Incomplete atom labelling, cannot make bond -101: [03:35:37] +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +58: [13:04:19] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +58: [13:04:19] SMILES Parse Error: check for mistakes around position 4: +58: [13:04:19] c%()ccccc%() +58: [13:04:19] ~~~^ +58: [13:04:19] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +58: [13:04:19] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +58: [13:04:19] SMILES Parse Error: check for mistakes around position 9: +58: [13:04:19] c%(100000)ccccc%(100000) +58: [13:04:19] ~~~~~~~~^ +58: [13:04:19] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +58: [13:04:19] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +93: [13:04:19] reactant 2 has no mapped atoms. +58: [13:04:19] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +93: [13:04:19] >> Atoms within one molecule have different RXN roles. +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +93: [13:04:19] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +93: [13:04:19] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +93: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +93: [13:04:19] SMARTS Parse Error: syntax error while parsing: ([C:2] +96: [13:04:19] Found a SCD/SED line with missing/empty SDT specification at line 34 +96: [13:04:19] Found a SCD/SED line with missing/empty SDT specification at line 36 +96: [13:04:19] Found a SCD/SED line with missing/empty SDT specification at line 38 +96: [13:04:19] Found a SCD/SED line with missing/empty SDT specification at line 40 +96: [13:04:19] Found a SCD/SED line with missing/empty SDT specification at line 42 +96: [13:04:19] Found a SCD/SED line with missing/empty SDT specification at line 87 +96: [13:04:19] Found a SCD/SED line with missing/empty SDT specification at line 89 +96: [13:04:19] Found a SCD/SED line with missing/empty SDT specification at line 91 +96: [13:04:19] Found a SCD/SED line with missing/empty SDT specification at line 93 +96: [13:04:19] Found a SCD/SED line with missing/empty SDT specification at line 95 +46: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +93: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [13:04:19] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +93: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +93: [13:04:19] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +93: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +101: [13:04:19] Incomplete atom labelling, cannot make bond +101: [13:04:19] 101: 101: **** 101: Invariant Violation @@ -21052,53 +20652,227 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/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-202503.1/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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000561C83B045D6 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000561C83B55A6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000561C83B56568 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000561C83B569CA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000561C83B28813 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000561C83B28AFC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000561C83AF882E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F1CFA233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x0000563758A465D6 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000563758A97A6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000563758A98568 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000563758A989CA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000563758A6A813 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000563758A6AAFC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000563758A3A82E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007FF651233CA8 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# 0x0000561C83AF8871 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000563758A3A871 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -72: [03:35:37] Finished: testRemoveHs() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -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] -60: Test -60: -60: Sotorasib_atropBad2.cxsmi -60: -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 - 73/238 Test #83: cdxmlParserCatchTest ................... Passed 0.16 sec +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +93: [13:04:19] reactant 0 has no mapped atoms. +93: [13:04:19] reactant 1 has no mapped atoms. +93: [13:04:19] reactant 3 has no mapped atoms. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 4 found multiple times. +93: [13:04:19] product atom-mapping number 5 found multiple times. +93: [13:04:19] product atom-mapping number 6 found multiple times. +93: [13:04:19] product atom-mapping number 7 found multiple times. +93: [13:04:19] product atom-mapping number 8 found multiple times. +93: [13:04:19] product atom-mapping number 12 found multiple times. +93: [13:04:19] product atom-mapping number 9 found multiple times. +93: [13:04:19] product atom-mapping number 10 found multiple times. +93: [13:04:19] product atom-mapping number 11 found multiple times. +93: [13:04:19] reactant 0 has no mapped atoms. +93: [13:04:19] reactant 1 has no mapped atoms. +93: [13:04:19] reactant 3 has no mapped atoms. +93: [13:04:19] reactant atom-mapping number 19 found multiple times. +93: [13:04:19] reactant atom-mapping number 25 found multiple times. +93: [13:04:19] reactant atom-mapping number 20 found multiple times. +93: [13:04:19] reactant atom-mapping number 21 found multiple times. +93: [13:04:19] reactant atom-mapping number 22 found multiple times. +93: [13:04:19] reactant atom-mapping number 23 found multiple times. +93: [13:04:19] reactant atom-mapping number 24 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [13:04:19] product atom-mapping number 5 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 4 found multiple times. +93: [13:04:19] product atom-mapping number 5 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 4 found multiple times. +93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [13:04:19] product atom-mapping number 5 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 4 found multiple times. +93: [13:04:19] product atom-mapping number 5 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 4 found multiple times. +93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 4 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 4 found multiple times. +93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 4 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 4 found multiple times. +93: F[C@](Cl)(Br)O[C@](F)(Cl)Br +93: [13:04:19] product atom-mapping number 4 found multiple times. +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 4 found multiple times. +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 4 found multiple times. +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] product atom-mapping number 4 found multiple times. +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +96: [13:04:19] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +70: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [13:04:19] Explicit valence for atom # 0 Al, 6, is greater than permitted +70: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: [13:04:19] Explicit valence for atom # 0 Al, 6, is greater than permitted +46: [13:04:19] Explicit valence for atom # 1 Si, 6, is greater than permitted +46: [13:04:19] Explicit valence for atom # 1 Si, 6, is greater than permitted +58: [13:04:19] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +46: [13:04:19] Explicit valence for atom # 0 P, 6, is greater than permitted +58: [13:04:19] SMILES Parse Error: check for mistakes around position 14: +58: [13:04:19] COc(c1)cccc1C# +58: [13:04:19] ~~~~~~~~~~~~~^ +58: [13:04:19] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +46: [13:04:19] Explicit valence for atom # 0 P, 6, is greater than permitted +58: [13:04:19] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +46: [13:04:19] Explicit valence for atom # 0 P, 7, is greater than permitted +58: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [13:04:19] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [13:04:19] SMILES Parse Error: check for mistakes around position 14: +58: [13:04:19] COc(c1)cccc1C# +58: [13:04:19] ~~~~~~~~~~~~~^ +46: [13:04:19] Explicit valence for atom # 0 P, 7, is greater than permitted +58: [13:04:19] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +46: [13:04:19] Explicit valence for atom # 1 As, 6, is greater than permitted +58: [13:04:19] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +58: [13:04:19] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +46: [13:04:19] Explicit valence for atom # 1 As, 6, is greater than permitted +58: [13:04:19] SMILES Parse Error: check for mistakes around position 14: +58: [13:04:19] COc(c1)cccc1C# +58: [13:04:19] ~~~~~~~~~~~~~^ +58: [13:04:19] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +46: [13:04:19] Explicit valence for atom # 1 As, 7, is greater than permitted +58: [13:04:19] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +58: [13:04:19] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +46: [13:04:19] Explicit valence for atom # 1 As, 7, is greater than permitted +46: [13:04:19] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [13:04:19] Explicit valence for atom # 0 Sb, 6, is greater than permitted +46: [13:04:19] Explicit valence for atom # 0 Sb, 7, is greater than permitted +46: [13:04:19] Explicit valence for atom # 0 Sb, 7, is greater than permitted +58: C=c1s/c2n(c1=O)CCCCCCC\N=2 +46: [13:04:19] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [13:04:19] Explicit valence for atom # 1 Bi, 6, is greater than permitted +46: [13:04:19] Explicit valence for atom # 1 Bi, 8, is greater than permitted +46: [13:04:19] Explicit valence for atom # 1 Bi, 8, is greater than permitted +58: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 +70: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +46: =============================================================================== +46: All tests passed (4479 assertions in 107 test cases) +46: +58: [13:04:19] SMILES Parse Error: extra close parentheses while parsing: C) +58: [13:04:19] SMILES Parse Error: check for mistakes around position 2: +58: [13:04:19] C) +58: [13:04:19] ~^ +58: [13:04:19] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' +96: [13:04:19] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 4 +93: [13:04:19] product atom-mapping number 3 found multiple times. +93: [13:04:19] product atom-mapping number 2 found multiple times. +93: [13:04:19] product atom-mapping number 1 found multiple times. +93: [13:04:19] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 4 +111: [13:04:19] ------------------------------------- +111: [13:04:19] Test Crippen parameter acquisition. +111: [13:04:19] done +111: [13:04:19] ------------------------------------- +111: [13:04:19] Test Crippen calculation. +96: [13:04:19] SMARTS Parse Error: unclosed ring for input: 'CC1' +96: [13:04:19] SMILES Parse Error: unclosed ring for input: 'CC1' +96: [13:04:19] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [13:04:19] product atom-mapping number 2 not found in reactants. +93: [13:04:19] product atom-mapping number 6 not found in reactants. +93: [13:04:19] product atom-mapping number 7 not found in reactants. +93: [13:04:19] product atom-mapping number 8 not found in reactants. +93: [13:04:19] product atom-mapping number 7 not found in reactants. +93: [13:04:19] product atom-mapping number 8 not found in reactants. +93: [13:04:19] product atom-mapping number 9 not found in reactants. +93: [13:04:19] product atom-mapping number 10 not found in reactants. +93: [13:04:19] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 6 + 71/238 Test #58: smiTest1 ............................... Passed 0.86 sec test 113 Start 113: testATF 113: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF 113: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 113: Test timeout computed to be: 1500 -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -72: [03:35:37] Finished: testGetItemText() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -60: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -96: [03:35:37] reactant 0 has no mapped atoms. -96: [03:35:37] product 0 has no mapped atoms. -96: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [03:35:37] Explicit valence for atom # 1 O, 5, is greater than permitted +83: [13:04:19] Incomplete atom labelling, cannot make bond 109: 21 -101: [03:35:37] Incomplete atom labelling, cannot make bond -101: [03:35:37] +93: [13:04:19] product atom-mapping number 7 not found in reactants. +93: [13:04:19] product atom-mapping number 8 not found in reactants. +93: [13:04:19] product atom-mapping number 9 not found in reactants. +93: [13:04:19] product atom-mapping number 10 not found in reactants. +93: [13:04:19] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 6 +96: [13:04:19] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [13:04:19] product atom-mapping number 2 not found in reactants. +112: [13:04:19] ---------------------------- +112: start test autocorr2D +101: [13:04:19] Incomplete atom labelling, cannot make bond +101: [13:04:19] 101: 101: **** 101: Invariant Violation @@ -21111,64 +20885,112 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/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-202503.1/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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000561C83B045D6 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000561C83B55A6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000561C83B56568 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000561C83B569CA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000561C83B28813 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000561C83B28AFC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000561C83AF882E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F1CFA233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x0000563758A465D6 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000563758A97A6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000563758A98568 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000563758A989CA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000563758A6A813 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000563758A6AAFC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000563758A3A82E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007FF651233CA8 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# 0x0000561C83AF8871 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000563758A3A871 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -111: [03:35:37] ------------------------------------- -111: [03:35:37] Test Crippen parameter acquisition. -112: [03:35:37] ---------------------------- -112: start test autocorr2D -96: =============================================================================== -96: All tests passed (722 assertions in 30 test cases) -96: - 74/238 Test #100: testChemTransforms ..................... Passed 0.09 sec + 72/238 Test #46: graphmolTestsCatch ..................... Passed 1.02 sec test 114 Start 114: testBCUT 114: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT 114: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 114: Test timeout computed to be: 1500 -111: [03:35:37] done -111: [03:35:37] ------------------------------------- -111: [03:35:37] Test Crippen calculation. -80: [03:35:37] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 - 75/238 Test #96: rxnTestCatch ........................... Passed 0.11 sec +96: [13:04:19] CX Extensions: Substance group hierarchy is not always preserved. +96: [13:04:19] CX Extensions: Substance group hierarchy is not always preserved. +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 + 73/238 Test #100: testChemTransforms ..................... Passed 0.33 sec test 115 Start 115: testEEM 115: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM 115: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 115: Test timeout computed to be: 1500 -80: [03:35:37] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[03:35:37] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -80: [03:35:37] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -80: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [03:35:37] Finished: testForwardSDSupplier() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testMissingCRSDSupplier() -72: [03:35:37] ----------------------------------------- +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] +70: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +111: [13:04:19] done +111: [13:04:19] ------------------------------------- +111: [13:04:19] Test Issue262: problems with Crippen calculation from pickles. +111: [13:04:19] done +111: [13:04:19] ------------------------------------- +111: [13:04:19] Test AMW calculation. +111: [13:04:19] done +111: [13:04:19] ------------------------------------- +111: [13:04:19] Test Exact MW calculation. +111: [13:04:19] done +111: [13:04:19] ------------------------------------- +111: [13:04:19] Test Labute ASA descriptors. +111: [13:04:19] done +111: [13:04:19] ------------------------------------- +111: [13:04:19] Test TPSA descriptors. +80: [13:04:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +83: [13:04:19] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [13:04:19] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +83: [13:04:19] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +30: ...[13:04:19] Molecule does not have explicit Hs. Consider calling AddHs() +60: Test +60: +60: RP-6306_atrop1.cxsmi +60: +60: Test +60: +60: RP-6306_atrop2.cxsmi +60: +60: Test +60: +60: RP-6306_atrop3.cxsmi +60: +60: Test +60: +60: RP-6306_atrop4.cxsmi +60: +60: Test +60: +60: RP-6306_atrop5.cxsmi +60: +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +72: [13:04:19] Finished: testSmilesSup() +72: [13:04:19] ----------------------------------------- 72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testIssue3482695() -72: [03:35:37] ----------------------------------------- +72: [13:04:19] ----------------------------------------- +72: [13:04:19] ------------------------------------------------------ +72: [13:04:19] SMILES Parse Error: syntax error while parsing: fail +72: [13:04:19] SMILES Parse Error: check for mistakes around position 1: +72: [13:04:19] fail +72: [13:04:19] ^ +72: [13:04:19] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +72: [13:04:19] ERROR: Smiles parse error on line 3 +72: [13:04:19] ERROR: Cannot create molecule from : 'fail' +72: [13:04:19] ------------------------------------------------------ +72: [13:04:19] ------------------------------------------------------ +72: [13:04:19] >>> This may result in an infinite loop. It should finish almost immediately: +72: [13:04:19] <<< done. +72: [13:04:19] Finished: testSmilesSupFromText() +72: [13:04:19] ----------------------------------------- 72: -72: [03:35:37] ----------------------------------------- -101: [03:35:37] Incomplete atom labelling, cannot make bond -101: [03:35:37] Incomplete atom labelling, cannot make bond -101: [03:35:37] Incomplete atom labelling, cannot make bond -101: [03:35:37] +72: [13:04:19] ----------------------------------------- +101: [13:04:19] Incomplete atom labelling, cannot make bond +101: [13:04:19] Incomplete atom labelling, cannot make bond +101: [13:04:19] Incomplete atom labelling, cannot make bond +101: [13:04:19] 101: 101: **** 101: Invariant Violation @@ -21181,68 +21003,83 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/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-202503.1/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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000561C83B045D6 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000561C83B55A6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000561C83B56568 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000561C83B569CA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000561C83B28813 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000561C83B28AFC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000561C83AF882E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F1CFA233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x0000563758A465D6 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000563758A97A6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000563758A98568 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000563758A989CA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000563758A6A813 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000563758A6AAFC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000563758A3A82E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007FF651233CA8 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# 0x0000561C83AF8871 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000563758A3A871 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -72: [03:35:37] ERROR: Cannot convert 'foo' to unsigned int on line 557 -72: [03:35:37] ERROR: moving to the beginning of the next molecule -72: [03:35:37] Finished: testIssue3525673() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 76/238 Test #113: testATF ................................ Passed 0.03 sec -72: [03:35:37] Finished: testBlankLinesInProps() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testSkipLines() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testGitHub23() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- +83: [13:04:19] Failed to parse XML fragment 5 node: b attribute: Order: 5 +83: [13:04:19] Invalid or missing fragment id from CDXML fragment, assigning new one... +96: [13:04:19] reactant 0 has no mapped atoms. +96: [13:04:19] product 0 has no mapped atoms. +114: [13:04:19] ------------------------------------- +114: [13:04:19] Basic BCUT tests. +96: [13:04:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [13:04:19] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [13:04:19] Explicit valence for atom # 1 O, 5, is greater than permitted +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +80: [13:04:19] 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.[13:04:19] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +80: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: [13:04:19] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +80: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +90: done +90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +90: processing2 +90: launch2 :0 +90: launch2 :1 +90: launch2 :2 +90: launch2 :3 +96: =============================================================================== +96: All tests passed (722 assertions in 30 test cases) +96: +83: =============================================================================== +83: All tests passed (263 assertions in 7 test cases) +83: + 74/238 Test #83: cdxmlParserCatchTest ................... Passed 0.64 sec test 116 Start 116: testPBF 116: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF 116: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 116: Test timeout computed to be: 1500 -72: [03:35:37] Finished: testGitHub88() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -70: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: [03:35:37] done -111: [03:35:37] ------------------------------------- -111: [03:35:37] Test Issue262: problems with Crippen calculation from pickles. -111: [03:35:37] done -111: [03:35:37] ------------------------------------- -111: [03:35:37] Test AMW calculation. -111: [03:35:37] done -111: [03:35:37] ------------------------------------- -111: [03:35:37] Test Exact MW calculation. -111: [03:35:37] done -111: [03:35:37] ------------------------------------- -111: [03:35:37] Test Labute ASA descriptors. -111: [03:35:37] done -111: [03:35:37] ------------------------------------- -111: [03:35:37] Test TPSA descriptors. 104: Finished 104: ----------------------- 104: Path retrieval +72: [13:04:19] Finished: testSmilesWriter() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- + 75/238 Test #96: rxnTestCatch ........................... Passed 0.44 sec +test 117 + Start 117: testRDFcustom + +117: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom +117: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +117: Test timeout computed to be: 1500 +60: Test +60: +60: RP-6306_atrop6.cxsmi +60: +60: Test +60: +60: RP-6306_atropBad1.cxsmi +60: +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +114: [13:04:19] done +114: [13:04:19] ------------------------------------- +114: [13:04:19] Larger BCUT tests. +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 104: Finished 104: ----------------------- 104: Path retrieval2 @@ -21252,18 +21089,10 @@ 104: Finished 104: ----------------------- 104: testUniqueSubgraphs2 -70: Atropisomers- 1 hits 3 misses -70: Final results: -70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses - 77/238 Test #70: testAtropisomers ....................... Passed 0.25 sec -test 117 - Start 117: testRDFcustom - -117: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom -117: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -117: Test timeout computed to be: 1500 -101: [03:35:37] Incomplete atom labelling, cannot make bond -101: [03:35:37] +95: 30000000 30000000 +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +101: [13:04:19] Incomplete atom labelling, cannot make bond +101: [13:04:19] 101: 101: **** 101: Invariant Violation @@ -21276,20 +21105,35 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/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-202503.1/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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000561C83B045D6 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000561C83B55A6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000561C83B56568 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000561C83B569CA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000561C83B28813 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000561C83B28AFC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000561C83AF882E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x00007F1CFA233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 4# 0x0000563758A465D6 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000563758A97A6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000563758A98568 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000563758A989CA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000563758A6A813 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000563758A6AAFC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000563758A3A82E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x00007FF651233CA8 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# 0x0000561C83AF8871 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000563758A3A871 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [03:35:37] + 76/238 Test #113: testATF ................................ Passed 0.12 sec +test 118 + Start 118: testRDF + +118: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF +118: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +118: Test timeout computed to be: 1500 +60: Test +60: +60: RP-6306_atropBad2.cxsmi +60: +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +101: [13:04:19] 101: 101: **** 101: Invariant Violation @@ -21303,70 +21147,53 @@ 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202503.1/obj-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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 5# 0x0000561C83AF95DD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000561C83B55A6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000561C83B56568 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000561C83B569CA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000561C83B28813 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000561C83B28AFC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000561C83AF882E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 12# 0x00007F1CFA233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +101: 5# 0x0000563758A3B5DD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000563758A97A6C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000563758A98568 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000563758A989CA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000563758A6A813 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000563758A6AAFC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000563758A3A82E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 12# 0x00007FF651233CA8 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# 0x0000561C83AF8871 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 14# 0x0000563758A3A871 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -93: [03:35:37] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 -114: [03:35:37] ------------------------------------- -114: [03:35:37] Basic BCUT tests. -72: [03:35:37] Finished: testGitHub2285() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -72: [03:35:37] ERROR: Smiles parse error on line 1 -72: [03:35:37] ERROR: Cannot create molecule from : 'c1ccccc' -72: [03:35:37] SMILES Parse Error: extra open parentheses while parsing: C(C -72: [03:35:37] SMILES Parse Error: check for mistakes around position 2: -72: [03:35:37] C(C -72: [03:35:37] ~^ -72: [03:35:37] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -72: [03:35:37] ERROR: Smiles parse error on line 3 -72: [03:35:37] ERROR: Cannot create molecule from : 'C(C' -72: [03:35:37] Explicit valence for atom # 1 C, 5, is greater than permitted -72: [03:35:37] ERROR: Could not sanitize molecule on line 5 -72: [03:35:37] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -72: [03:35:37] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:35:37] ERROR: Could not sanitize molecule ending on line 21 -72: [03:35:37] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:35:37] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:35:37] ERROR: Could not sanitize molecule ending on line 21 -72: [03:35:37] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:35:37] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:35:37] ERROR: Could not sanitize molecule ending on line 21 -72: [03:35:37] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:35:37] ERROR: Atom line too short: ' -9.6' on line 28 -72: [03:35:37] ERROR: moving to the beginning of the next molecule -72: [03:35:37] Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:35:37] ERROR: Could not sanitize molecule ending on line 21 -72: [03:35:37] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -72: [03:35:37] ERROR: Atom line too short: ' -9.6' on line 28 -72: [03:35:37] ERROR: moving to the beginning of the next molecule -72: [03:35:37] Finished: testGitHub2479() -72: [03:35:37] ----------------------------------------- -72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Ignoring invalid chirality label: '7_S_8_9_6_10' -72: [03:35:37] Finished: testGitHub2881() -72: [03:35:37] ----------------------------------------- +101: =============================================================================== +101: All tests passed (675 assertions in 10 test cases) +101: +90: done +90: preprocessing 3 +90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 +90: processing3 +90: launch3 :0 +90: launch3 :1 +90: launch3 :2 +90: launch3 :3 +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 + 77/238 Test #101: chemTransformsTestCatch ................ Passed 0.42 sec +test 119 + Start 119: testMORSE + +119: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE +119: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +119: Test timeout computed to be: 1500 +72: [13:04:19] Finished: testSDWriter() +72: [13:04:19] ----------------------------------------- 72: -72: [03:35:37] ----------------------------------------- -72: [03:35:37] Finished: testGitHub3517() -72: [03:35:37] ----------------------------------------- +72: [13:04:19] ----------------------------------------- +93: [13:04:19] 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 +115: =>start test EEM +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 0 +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [13:04:19] Finished: testSDSupplierEnding() +72: [13:04:19] ----------------------------------------- 72: -95: 30000000 30000000 - 78/238 Test #72: testMolSupplier ........................ Passed 0.26 sec +72: [13:04:19] ----------------------------------------- 107: Warning: molecule failed filter 107: Warning: molecule failed filter: reason hzone_phenol_A(479) 107: v = { @@ -21386,12 +21213,6 @@ 107: 1,22}, 107: 2,20}, 107: 3,19}, -test 118 - Start 118: testRDF - -118: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF -118: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -118: Test timeout computed to be: 1500 107: 4,25}, 107: 5,24}, 107: 6,18}, @@ -21431,42 +21252,28 @@ 107: 11,17}, 107: 12,16}, 107: } -60: Test -60: -60: Sotorasib_3d.cxsmi -60: -60: Test -60: -60: ZM374979_atrop1.cxsmi -60: -60: Test -60: -60: ZM374979_atrop2.cxsmi -60: -60: Test -60: -60: ZM374979_atrop3.cxsmi -60: -60: Test -60: -60: ZM374979_atrop4.cxsmi -60: -60: Test -60: -60: ZM374979_atropBad1.cxsmi -60: -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -101: =============================================================================== -101: All tests passed (675 assertions in 10 test cases) -101: -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +116: [13:04:19] ------------------------------------- +116: [13:04:19] Basic PBF tests. +72: [13:04:19] Finished: testSuppliersEmptyFile() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +72: [13:04:19] Finished: testCisTrans() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 107: Warning: molecule failed filter -116: [03:35:37] ------------------------------------- -116: [03:35:37] Basic PBF tests. - 79/238 Test #101: chemTransformsTestCatch ................ Passed 0.13 sec -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +89: Randomness seeded to: 1381384157 +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 107: Warning: molecule failed filter: reason keto_keto_gamma(5) 107: v = { 107: 0,0}, @@ -21496,24 +21303,179 @@ 107: 10,15}, 107: 11,16}, 107: } -test 119 - Start 119: testMORSE - -119: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE -119: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -119: Test timeout computed to be: 1500 -114: [03:35:37] done -114: [03:35:37] ------------------------------------- -114: [03:35:37] Larger BCUT tests. -115: =>start test EEM -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 0 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -75: [03:35:37] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +72: [13:04:19] Finished: testStereoRound() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +72: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [13:04:19] Finished: testIssue226() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111: [13:04:19] done +111: [13:04:19] ------------------------------------- +111: [13:04:19] Test Lipinski parameters. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [13:04:19] Finished: testTDTSupplier1() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +72: [13:04:19] Finished: testTDTSupplier2() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +75: [13:04:19] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +72: [13:04:19] Finished: testTDTSupplier3() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +72: [13:04:19] Finished: testSDSupplierFromText() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +72: [13:04:19] ERROR: Problems encountered parsing data fields +72: [13:04:19] ERROR: moving to the beginning of the next molecule +72: [13:04:19] ERROR: Problems encountered parsing data fields +72: [13:04:19] ERROR: moving to the beginning of the next molecule +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +72: [13:04:19] Spurious data before the first property will be ignored +72: [13:04:19] Property will be truncated after the first blank line +72: [13:04:19] Property will be truncated after the first blank line +72: [13:04:19] Property will be truncated after the first blank line +72: [13:04:19] Finished: testSDSupplierStrLax1() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +72: [13:04:19] ERROR: Problems encountered parsing data fields +72: [13:04:19] ERROR: moving to the beginning of the next molecule +72: [13:04:19] Property will be truncated after the first blank line +72: [13:04:19] Finished: testSDSupplierStrLax2() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +72: [13:04:19] ERROR: Problems encountered parsing data fields +72: [13:04:19] ERROR: moving to the beginning of the next molecule +72: [13:04:19] ERROR: Problems encountered parsing data fields +72: [13:04:19] ERROR: moving to the beginning of the next molecule +72: [13:04:19] Spurious data before the first property will be ignored +72: [13:04:19] Property will be truncated after the first blank line +72: [13:04:19] Property will be truncated after the first blank line +72: [13:04:19] Property will be truncated after the first blank line +72: [13:04:19] Finished: testSDSupplierFromTextStrLax1() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +72: [13:04:19] ERROR: Problems encountered parsing data fields +72: [13:04:19] ERROR: moving to the beginning of the next molecule 75: 0.40201265 0.40201265 75: -0.13299436 -0.13299436 75: 1.00000017 1.00000017 @@ -21521,7 +21483,6 @@ 75: 0.9973909 0.9973909 75: 1.00000003 1.00000003 75: 0.36613799 0.36613799 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 75: 2.1107185 2.1107185 75: 0.99999982 0.99999982 75: 2.48696157 2.48696157 @@ -21536,180 +21497,700 @@ 75: 3.0077234 3.0077234 75: 0.37399312 0.37399312 75: -0.07713336 -0.07713336 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -75: [03:35:37] bond with order 0 found on line 11. This is not part of the MDL specification. -75: [03:35:37] bond with order 0 found on line 16. This is not part of the MDL specification. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -93: [03:35:37] product atom-mapping number 17 not found in reactants. -93: [03:35:37] product atom-mapping number 18 not found in reactants. -93: [03:35:37] mapped atoms in the reactants were not mapped in the products. +72: [13:04:19] Property will be truncated after the first blank line +72: [13:04:19] Finished: testSDSupplierFromTextStrLax2() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +72: [13:04:19] Finished: testIssue265() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +72: [13:04:19] ERROR: End of data field name not found +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +72: [13:04:19] ERROR: moving to the beginning of the next molecule +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +72: [13:04:19] Explicit valence for atom # 0 F, 2, is greater than permitted +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +72: [13:04:19] ERROR: Could not sanitize molecule ending on line 16 +72: [13:04:19] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +75: [13:04:19] bond with order 0 found on line 11. This is not part of the MDL specification. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +75: [13:04:19] bond with order 0 found on line 16. This is not part of the MDL specification. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +72: [13:04:19] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +72: [13:04:19] ERROR: moving to the beginning of the next molecule +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [13:04:19] ERROR: Bond line too short: 'M END' on line 18 +72: [13:04:19] ERROR: moving to the beginning of the next molecule +72: [13:04:19] Finished: testSDErrorHandling() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +93: [13:04:19] product atom-mapping number 17 not found in reactants. +93: [13:04:19] product atom-mapping number 18 not found in reactants. +93: [13:04:19] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 12 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [13:04:19] Finished: testIssue381() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [13:04:19] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +72: [13:04:19] Finished: testSetStreamIndices() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [13:04:19] Finished: testMixIterAndRandom() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: build: +72: [13:04:19] Finished: testRemoveHs() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 60: Test 60: -60: Mrtx1719_3d.cxsmi +60: RP-6306_3d.cxsmi 60: 60: Test 60: -60: Mrtx1719_atrop1.cxsmi +60: Sotorasib_atrop1.cxsmi 60: 60: Test 60: -60: Mrtx1719_atrop2.cxsmi +60: Sotorasib_atrop2.cxsmi 60: 60: Test 60: -60: Mrtx1719_atrop3.cxsmi +60: Sotorasib_atrop3.cxsmi 60: 60: Test 60: -60: Mrtx1719_atrop4.cxsmi +60: Sotorasib_atrop4.cxsmi 60: 60: Test 60: -60: Mrtx1719_atropBad1.cxsmi +60: Sotorasib_atrop5.cxsmi 60: -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -65: [03:35:37] Warning: stereochemistry around double bond may be incorrect in depiction. -90: done -60: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -90: processing2 -90: launch2 :0 -90: launch2 :1 -90: launch2 :2 -90: launch2 :3 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 80/238 Test #75: testMolWriter .......................... Passed 0.30 sec -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored + 78/238 Test #75: testMolWriter .......................... Passed 0.94 sec +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. test 120 Start 120: test3D 120: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D 120: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 120: Test timeout computed to be: 1500 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: [03:35:37] done -111: [03:35:37] ------------------------------------- -111: [03:35:37] Test Lipinski parameters. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [03:35:37] ------------------------------------- -120: [03:35:37] Basic PMI tests. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +72: [13:04:19] Finished: testGetItemText() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +60: [13:04:19] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: Test +60: +60: Sotorasib_atropBad1.cxsmi +60: +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: [13:04:19] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +60: Test +60: +60: Sotorasib_atropBad2.cxsmi +60: +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 90: done -90: preprocessing 3 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 -90: processing3 -90: launch3 :0 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: launch3 :1 -90: launch3 :2 -90: launch3 :3 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: Randomness seeded to: 1502982509 -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +90: [13:04:19] done +90: [13:04:19] ------------------------------------- +90: [13:04:19] Test GitHub issue 15 +90: [13:04:19] done +90: [13:04:19] ------------------------------------- +90: [13:04:19] Test GitHub issue 409 +90: [13:04:19] done +90: [13:04:19] ------------------------------------- +90: [13:04:19] Test chiral matching +90: [13:04:19] done +90: [13:04:19] ------------------------------------- +90: [13:04:19] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +90: [13:04:19] done +90: [13:04:19] ------------------------------------- +90: [13:04:19] Test dative-bond matching +90: [13:04:19] done +90: [13:04:19] ------------------------------------- +90: [13:04:19] Test cis/trans matching +72: [13:04:19] Finished: testForwardSDSupplier() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +72: [13:04:19] Finished: testMissingCRSDSupplier() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +120: [13:04:19] ------------------------------------- +120: [13:04:19] Basic PMI tests. +30: ......[13:04:19] Molecule does not have explicit Hs. Consider calling AddHs() +72: [13:04:19] Finished: testIssue3482695() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +60: [13:04:19] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [13:04:19] ERROR: Cannot convert 'foo' to unsigned int on line 557 +72: [13:04:19] ERROR: moving to the beginning of the next molecule +90: [13:04:19] done +90: [13:04:19] ------------------------------------- +90: [13:04:19] Test cis/trans matching part 2 +90: [13:04:19] done +90: [13:04:19] ------------------------------------- +90: [13:04:19] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +72: [13:04:19] Finished: testIssue3525673() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +90: [13:04:19] done +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [13:04:19] Finished: testBlankLinesInProps() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +90: [13:04:19] ------------------------------------- +90: [13:04:19] Testing matching E/Z against Cis/Trans stereo bonds +72: [13:04:19] Finished: testSkipLines() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +72: [13:04:19] Finished: testGitHub23() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +72: [13:04:19] Finished: testGitHub88() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +90: [13:04:19] +90: +90: **** +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +90: Pre-condition Violation +90: matches must not be empty +90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +90: Failed Expression: !matches.empty() +90: ---------- +90: Stacktrace: +90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/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-202503.1/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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +90: 4# 0x0000555D0315B37A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x0000555D0314BBE1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x00007F9E2EC33CA8 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# 0x0000555D0314BD21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: ---------- +90: **** +90: +90: [13:04:19] +90: +90: **** +90: Pre-condition Violation +90: matches must not be empty +90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +90: Failed Expression: !matches.empty() +90: ---------- +90: Stacktrace: +90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/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-202503.1/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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +90: 4# 0x0000555D03146423 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x0000555D0314BBE1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x00007F9E2EC33CA8 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# 0x0000555D0314BD21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: ---------- +90: **** +90: +90: [13:04:19] ------------------------------------- +90: [13:04:19] Test substructure matching with a pathological case for symmetric SSSR +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +90: [13:04:19] ------------------------------------- +90: [13:04:19] Test isAtomTerminalRGroupOrQueryHydrogen +93: [13:04:19] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +93: [13:04:19] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 79/238 Test #90: testSubstructMatch ..................... Passed 0.89 sec +test 121 + Start 121: testWHIM + +121: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM +121: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +121: Test timeout computed to be: 1500 +93: [13:04:19] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +93: ------------- +93: CCOc1ccccc1 +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [13:04:19] Finished: testGitHub2285() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +72: [13:04:19] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +72: [13:04:19] ERROR: Smiles parse error on line 1 +72: [13:04:19] ERROR: Cannot create molecule from : 'c1ccccc' +72: [13:04:19] SMILES Parse Error: extra open parentheses while parsing: C(C +72: [13:04:19] SMILES Parse Error: check for mistakes around position 2: +72: [13:04:19] C(C +72: [13:04:19] ~^ +72: [13:04:19] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +72: [13:04:19] ERROR: Smiles parse error on line 3 +72: [13:04:19] ERROR: Cannot create molecule from : 'C(C' +72: [13:04:19] Explicit valence for atom # 1 C, 5, is greater than permitted +72: [13:04:19] ERROR: Could not sanitize molecule on line 5 +72: [13:04:19] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +72: [13:04:19] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [13:04:19] ERROR: Could not sanitize molecule ending on line 21 +72: [13:04:19] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [13:04:19] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [13:04:19] ERROR: Could not sanitize molecule ending on line 21 +72: [13:04:19] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [13:04:19] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [13:04:19] ERROR: Could not sanitize molecule ending on line 21 +72: [13:04:19] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [13:04:19] ERROR: Atom line too short: ' -9.6' on line 28 +72: [13:04:19] ERROR: moving to the beginning of the next molecule +72: [13:04:19] Explicit valence for atom # 1 F, 2, is greater than permitted +72: [13:04:19] ERROR: Could not sanitize molecule ending on line 21 +72: [13:04:19] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +72: [13:04:19] ERROR: Atom line too short: ' -9.6' on line 28 +72: [13:04:19] ERROR: moving to the beginning of the next molecule +72: [13:04:19] Finished: testGitHub2479() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +72: [13:04:19] Ignoring invalid chirality label: '7_S_8_9_6_10' +72: [13:04:19] Finished: testGitHub2881() +72: [13:04:19] ----------------------------------------- +72: +72: [13:04:19] ----------------------------------------- +72: [13:04:19] Finished: testGitHub3517() +72: [13:04:19] ----------------------------------------- +72: +70: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 80/238 Test #72: testMolSupplier ........................ Passed 1.17 sec +test 122 + Start 122: testGETAWAY + +122: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY +122: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +122: Test timeout computed to be: 1500 +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: Atropisomers- 1 hits 3 misses +70: Final results: +70: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses + 81/238 Test #70: testAtropisomers ....................... Passed 1.22 sec +test 123 + Start 123: testAUTOCORR3D + +123: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D +123: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +123: Test timeout computed to be: 1500 +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +102: Randomness seeded to: 565981184 +102: =============================================================================== +102: All tests passed (93 assertions in 13 test cases) +102: + 82/238 Test #102: tautomerQueryTestCatch ................. Passed 0.84 sec +test 124 + Start 124: testCoulombMat + +124: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat +124: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +124: Test timeout computed to be: 1500 +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +65: [13:04:20] Warning: stereochemistry around double bond may be incorrect in depiction. +91: Randomness seeded to: 1718308135 +91: =============================================================================== +91: All tests passed (242 assertions in 12 test cases) +91: + 83/238 Test #91: substructTestCatch ..................... Passed 0.98 sec +test 125 + Start 125: descriptorsTestCatch + +125: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch +125: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +125: Test timeout computed to be: 1500 +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 100 +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: Test +60: +60: Sotorasib_3d.cxsmi +60: +60: Test +60: +60: ZM374979_atrop1.cxsmi +60: +60: Test +60: +60: ZM374979_atrop2.cxsmi +60: +60: Test +60: +60: ZM374979_atrop3.cxsmi +60: +60: Test +60: +60: ZM374979_atrop4.cxsmi +60: +60: Test +60: +60: ZM374979_atropBad1.cxsmi +60: +60: [13:04:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [13:04:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +60: [13:04:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [13:04:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +124: ===================== Testing CoulombMat ======================= +111: [13:04:20] done +111: [13:04:20] ------------------------------------- +111: [13:04:20] Test VSA descriptors. +111: [13:04:20] done +111: [13:04:20] ------------------------------------- +111: [13:04:20] Test molecular formula calculation. +60: [13:04:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +111: [13:04:20] done +111: [13:04:20] ------------------------------------- +111: [13:04:20] Test Issue 3415534. +111: [13:04:20] done +111: [13:04:20] ------------------------------------- +111: [13:04:20] Test Issue3433771: Bad definition for Crippen atom type O11. +111: [13:04:20] done +111: [13:04:20] ------------------------------------- +111: [13:04:20] Test multithreading +111: reading molecules +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] 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 + 84/238 Test #124: testCoulombMat ......................... Passed 0.07 sec +test 126 + Start 126: pyMolDescriptors + +126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" +126: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap +126: Test timeout computed to be: 1500 +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +30: ... +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +30: ---------------------------------------------------------------------- +30: Ran 12 tests in 0.821s +30: +30: OK +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] 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: [13:04:20] test on : 365 molecules done +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: Test +60: +60: Mrtx1719_3d.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop1.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop2.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop3.cxsmi +60: +60: Test +60: +60: Mrtx1719_atrop4.cxsmi +60: +60: Test +60: +60: Mrtx1719_atropBad1.cxsmi +60: +60: [13:04:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [13:04:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +60: [13:04:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +60: [13:04:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +103: ..... +103: ---------------------------------------------------------------------- +103: Ran 5 tests in 0.188s +103: +103: OK +104: Finished +104: ----------------------- +104: testRootedSubgraphs +104: Finished +104: ----------------------- +104: testRootedPaths +104: Finished +60: [13:04:20] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +125: Randomness seeded to: 4224906084 +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 +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 85/238 Test #65: testDepictor ........................... Passed 3.54 sec +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] 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 ASN157A does not match expected count +test 127 + Start 127: pyMolDescriptors3D + +127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/test3D.py" +127: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap +127: Test timeout computed to be: 1500 +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] 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 + 86/238 Test #104: testSubgraphs1 ......................... Passed 3.04 sec +test 128 + Start 128: testFingerprints + +128: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints +128: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +128: Test timeout computed to be: 1500 +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: badWedgeError.sdf @@ -22022,117 +22503,17 @@ 68: 68: MulticenterSgroup.mrv 68: -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -68: [03:35:37] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [03:35:37] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -102: Randomness seeded to: 2920054303 -102: =============================================================================== -102: All tests passed (93 assertions in 13 test cases) -102: -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 81/238 Test #65: testDepictor ........................... Passed 0.41 sec - 82/238 Test #102: tautomerQueryTestCatch ................. Passed 0.24 sec -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -test 121 - Start 121: testWHIM - -121: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM -121: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -121: Test timeout computed to be: 1500 -test 122 - Start 122: testGETAWAY - -122: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY -122: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -122: Test timeout computed to be: 1500 -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [13:04:22] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +68: [13:04:22] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +35: [13:04:22] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. 68: Test 68: 68: GenericSgroup.mrv @@ -22165,7 +22546,7 @@ 68: 68: MarvinBadMissingMolID.mrv 68: -68: [03:35:37] +68: [13:04:22] 68: 68: **** 68: Test Assert @@ -22176,12 +22557,12 @@ 68: Stacktrace: 68: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 68: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -68: 2# 0x000055846C33A22F in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 3# 0x000055846C34169C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 4# 0x000055846C32EA5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -68: 5# 0x00007F6FA8433CA8 in /lib/x86_64-linux-gnu/libc.so.6 +68: 2# 0x000055A4731E322F in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 3# 0x000055A4731EA69C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 4# 0x000055A4731D7A5D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 5# 0x00007F5039233CA8 in /lib/x86_64-linux-gnu/libc.so.6 68: 6# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -68: 7# 0x000055846C32EBE1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +68: 7# 0x000055A4731D7BE1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 68: ---------- 68: **** 68: @@ -22195,47 +22576,21 @@ 68: MarvinBadX2.mrv 68: 68: The values x2 and y2 must be large floats in MRV file -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: MarvinBadY2.mrv 68: 68: The values x2 and y2 must be large floats in MRV file +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: MarvinBadStereoGroupsAbs.mrv 68: 68: Unrecognized group definition -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: MarvinBadElementType.mrv @@ -22258,6 +22613,18 @@ 68: MarvinBadMissingSruMolID.mrv 68: 68: Expected a molID in MRV file +99: .[13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- 68: Test 68: 68: MarvinBadMissingSruID.mrv @@ -22279,19 +22646,6 @@ 68: MarvinBadSruAtomRef.mrv 68: 68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -93: [03:35:37] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: [03:35:37] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: -93: [03:35:37] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: MarvinBadSruID.mrv @@ -22305,212 +22659,580 @@ 68: MarvinBadSruAtomRef.mrv 68: 68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -93: ------------- 68: Test 68: 68: MarvinBadSruAtomRef.mrv 68: 68: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -93: CCOc1ccccc1 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: 68: MarvinBadSruConnect.mrv 68: 68: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 68: Test 68: 68: MarvinBadSupAttachAtom.mrv 68: 68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 68: Test 68: 68: MarvinBadSupAttachBond.mrv 68: 68: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: Atoms: +128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: 1 conj?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +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: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: 1 conj?: 1 +128: 9 8->10 order: a conj?: 1 aromatic?: 1 +128: 10 10->1 order: a conj?: 1 aromatic?: 1 +128: 11 7->3 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: SMI: Oc1cc2[nH]cnc2c(O)n1 +128: Atoms: +128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: 1 conj?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +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: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: 1 conj?: 1 +128: 9 8->10 order: a conj?: 1 aromatic?: 1 +128: 10 10->1 order: a conj?: 1 aromatic?: 1 +128: 11 7->3 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: c1(O)cc2[nH]cnc2c(O)n1 +128: Atoms: +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 +128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: 1 conj?: 1 +128: 1 0->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +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: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: 1 conj?: 1 +128: 9 8->10 order: a conj?: 1 aromatic?: 1 +128: 10 10->0 order: a conj?: 1 aromatic?: 1 +128: 11 7->3 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: c1c(O)nc(O)c2c1[nH]cn2 +128: Atoms: +128: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 3 7 N chg: 0 deg: 2 exp: 3 imp: 0 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 +128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 7 6 C chg: 0 deg: 3 exp: 4 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 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: a conj?: 1 aromatic?: 1 +128: 1 1->2 order: 1 conj?: 1 +128: 2 1->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: a conj?: 1 aromatic?: 1 +128: 4 4->5 order: 1 conj?: 1 +128: 5 4->6 order: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: a conj?: 1 aromatic?: 1 +128: 9 9->10 order: a conj?: 1 aromatic?: 1 +128: 10 7->0 order: a conj?: 1 aromatic?: 1 +128: 11 10->6 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. 68: Test 68: 68: MarvinBadSupAttachOrder.mrv 68: 68: Order for an AttachmentPoint definition must be an integer in MRV file -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 68: Test 68: 68: MarvinBadSupAttachAtom.mrv 68: 68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 68: Test 68: 68: MarvinBadSupAttachAtom.mrv 68: 68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 68: Test 68: 68: MarvinBadSupAttachAtom.mrv 68: 68: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +116: [13:04:22] done +116: [13:04:22] ------------------------------------- +116: [13:04:22] PBF edge cases. 68: Test 68: 68: MarvinBadSupMissingAttachBond.mrv 68: 68: No attachment point found for bond to the condensed atom in a superatomSgroup -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 68: Test 68: 68: MarvinBadSupMissingAttachOrder.mrv 68: 68: Expected atom, order and bond, for an AttachmentPoint definition in MRV file -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [03:35:37] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 100 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: [03:35:37] == testCartesianProduct -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -30: ......[03:35:37] Molecule does not have explicit Hs. Consider calling AddHs() -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[03:35:37] == testEnumerateLibrary -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] 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-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> -98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) -98: ResourceWarning: Enable tracemalloc to get the object allocation traceback -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: .[03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: Finished -104: ----------------------- -104: testRootedSubgraphs -104: Finished -104: ----------------------- -104: testRootedPaths -104: Finished -99: .[03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. - 83/238 Test #104: testSubgraphs1 ......................... Passed 0.30 sec -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: SMI: c12cc(O)nc(O)c1nc[nH]2 +128: Atoms: +128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 3 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +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 +128: 7 6 C chg: 0 deg: 3 exp: 4 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 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: a conj?: 1 aromatic?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: 1 conj?: 1 +128: 3 2->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 +128: 6 5->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: a conj?: 1 aromatic?: 1 +128: 9 9->10 order: a conj?: 1 aromatic?: 1 +128: 10 7->0 order: a conj?: 1 aromatic?: 1 +128: 11 10->0 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: [nH]1c2cc(O)nc(O)c2nc1 +128: Atoms: +128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +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 +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 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: 1 conj?: 1 +128: 4 3->5 order: a conj?: 1 aromatic?: 1 +128: 5 5->6 order: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: 1 conj?: 1 +128: 7 6->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: a conj?: 1 aromatic?: 1 +128: 9 9->10 order: a conj?: 1 aromatic?: 1 +128: 10 10->0 order: a conj?: 1 aromatic?: 1 +128: 11 8->1 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: c1[nH]c2cc(O)nc(O)c2n1 +128: Atoms: +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 +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 +128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 8 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: a conj?: 1 aromatic?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: a conj?: 1 aromatic?: 1 +128: 4 4->5 order: 1 conj?: 1 +128: 5 4->6 order: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: 1 conj?: 1 +128: 8 7->9 order: a conj?: 1 aromatic?: 1 +128: 9 9->10 order: a conj?: 1 aromatic?: 1 +128: 10 10->0 order: a conj?: 1 aromatic?: 1 +128: 11 9->2 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: n1c[nH]c2cc(O)nc(O)c21 +128: Atoms: +128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +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 +128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 10 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: a conj?: 1 aromatic?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +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 +128: 6 5->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: 1 conj?: 1 +128: 9 8->10 order: a conj?: 1 aromatic?: 1 +128: 10 10->0 order: a conj?: 1 aromatic?: 1 +128: 11 10->3 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: c12c(cc(O)nc1O)[nH]cn2 +128: Atoms: +128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +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 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: a conj?: 1 aromatic?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +128: 3 3->4 order: 1 conj?: 1 +128: 4 3->5 order: a conj?: 1 aromatic?: 1 +128: 5 5->6 order: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: 1 conj?: 1 +128: 7 1->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: a conj?: 1 aromatic?: 1 +128: 9 9->10 order: a conj?: 1 aromatic?: 1 +128: 10 6->0 order: a conj?: 1 aromatic?: 1 +128: 11 10->0 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: c1(O)c2c(cc(O)n1)[nH]cn2 +128: Atoms: +128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +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 +128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +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 +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 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: 1 conj?: 1 +128: 1 0->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +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 +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 +128: 9 9->10 order: a conj?: 1 aromatic?: 1 +128: 10 7->0 order: a conj?: 1 aromatic?: 1 +128: 11 10->2 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: Oc1c2c(cc(O)n1)[nH]cn2 +128: Atoms: +128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +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 +128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +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 +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 +128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: Bonds: +128: 0 0->1 order: 1 conj?: 1 +128: 1 1->2 order: a conj?: 1 aromatic?: 1 +128: 2 2->3 order: a conj?: 1 aromatic?: 1 +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 +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 +128: 9 9->10 order: a conj?: 1 aromatic?: 1 +128: 10 7->1 order: a conj?: 1 aromatic?: 1 +128: 11 10->2 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: SMI: n1c(O)cc2[nH]cnc2c1O +128: Atoms: +128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +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 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 6 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 +128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 +128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 +128: 10 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 +128: Bonds: +128: 0 0->1 order: a conj?: 1 aromatic?: 1 +128: 1 1->2 order: 1 conj?: 1 +128: 2 1->3 order: a conj?: 1 aromatic?: 1 +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: a conj?: 1 aromatic?: 1 +128: 6 6->7 order: a conj?: 1 aromatic?: 1 +128: 7 7->8 order: a conj?: 1 aromatic?: 1 +128: 8 8->9 order: a conj?: 1 aromatic?: 1 +128: 9 9->10 order: 1 conj?: 1 +128: 10 9->0 order: a conj?: 1 aromatic?: 1 +128: 11 8->4 order: a conj?: 1 aromatic?: 1 +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +128: +128: +128: +128: +128: +128: +128: +128: +128: ------------------- +128: +99: .[13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. 99: () 99: ******************************************** 99: $RXN @@ -22874,18 +23596,92 @@ 99: 1 2 1 0 99: M ISO 2 1 1 2 2 99: M END -99: [03:35:37] reactant 0 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] product 0 has no mapped atoms. -99: [03:35:37] Could not find RLabel mapping for atom: 0 in template: 1 -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. -99: [03:35:37] reactant 1 has no mapped atoms. +99: [13:04:22] reactant 0 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] product 0 has no mapped atoms. +99: [13:04:22] Could not find RLabel mapping for atom: 0 in template: 1 +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. +99: [13:04:22] reactant 1 has no mapped atoms. 99: .. 99: ---------------------------------------------------------------------- -99: Ran 4 tests in 0.019s +99: Ran 4 tests in 0.117s 99: 99: OK +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +109: [13:04:22] +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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 2# 0x00007F8F98A74DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 4# 0x000056321E9A11FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x000056321E99E6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007F8F97E33CA8 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# 0x000056321E99E7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: ---------- +109: **** +109: +109: [13:04:22] +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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 2# 0x00007F8F98A74DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 4# 0x000056321E9A11FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x000056321E99E6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007F8F97E33CA8 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# 0x000056321E99E7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: ---------- +109: **** +109: +109: [13:04:22] +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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +109: 2# 0x00007F8F98A74DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 4# 0x000056321E9A11FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x000056321E99E6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x00007F8F97E33CA8 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# 0x000056321E99E7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: ---------- +109: **** +109: + 87/238 Test #109: testFragCatalog ........................ Passed 3.08 sec +test 129 + Start 129: testMHFPFingerprint + +129: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint +129: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +129: Test timeout computed to be: 1500 99: 99: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 99: $RXN @@ -22940,32 +23736,523 @@ 99: M END 99: 99: $RXN Failed -test 123 - Start 123: testAUTOCORR3D +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test Morgan Fingerprints. +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test Morgan Fingerprints using fromAtoms argument. +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test Morgan Fingerprints as bit vects. +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test Morgan Fingerprints with feature invariants. + 88/238 Test #107: filterCatalogTest ...................... Passed 3.18 sec +test 130 + Start 130: testFingerprintGenerators -123: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D -123: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -123: Test timeout computed to be: 1500 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -35: [03:35:37] Maximum BFS search size exceeded. -35: This is likely due to a highly symmetric fused ring system. -103: ..... -103: ---------------------------------------------------------------------- -103: Ran 5 tests in 0.048s -103: -103: OK -97: ...[03:35:37] +130: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators +130: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +130: Test timeout computed to be: 1500 +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +92: Randomness seeded to: 2195718472 +92: =============================================================================== +92: All tests passed (11480 assertions in 38 test cases) +92: +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test additional Morgan fingerprints options. +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test Atom Codes. +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test Atom Pairs. +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test Atom Pairs part 2. +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test Topological Torsions. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test Bulk Topological Torsions. + 89/238 Test #92: testGenericGroups ...................... Passed 3.39 sec +test 131 + Start 131: fpTestCatch + +131: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch +131: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +131: Test timeout computed to be: 1500 +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +129: [13:04:22] ------------------------------------- +129: [13:04:22] Test MHFP fingerprint encoder initialization +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +98: [13:04:22] == testCartesianProduct +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 200 +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] 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. + 90/238 Test #103: pyTautomerQuery ........................ Passed 3.30 sec +test 132 + Start 132: fpGenTestCatch + +132: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch +132: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +132: Test timeout computed to be: 1500 +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +68: Test +68: +68: marvin03.mrv +68: +68: Test +68: +68: Cubane.mrv +68: +68: Test +68: +68: FalseAtropisomer.mrv +68: +68: Test +68: +68: AtropEnhancedStereo.mrv +68: +68: Test +68: +68: AtropManyChirals.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced2.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced3.mrv +68: +68: Test +68: +68: AtropManyChiralsEnhanced4.mrv +68: +68: Test +68: +68: BMS-986142_3d_chiral.mrv +68: +68: Test +68: +68: BMS-986142_3d.mrv +68: +68: Test +68: +68: BMS-986142_atrop1.mrv +68: +68: Test +68: +68: BMS-986142_atrop2.mrv +68: +68: Test +68: +68: BMS-986142_atrop3.mrv +68: +68: Test +68: +68: BMS-986142_atrop4.mrv +68: +68: Test +68: +68: BMS-986142_atrop5.mrv +68: +68: [13:04:22] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [13:04:22] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test atom-pair fp generator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +98: .[13:04:22] == testEnumerateLibrary +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test atom-pair fp generator with different arguments +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +130: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +130: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +130: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +130: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +130: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +130: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +68: Test +68: +68: BMS-986142_atrop6.mrv +68: +68: Test +68: +68: BMS-986142_atrop7.mrv +68: +68: Test +68: +68: BMS-986142_atrop8.mrv +68: +68: [13:04:22] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [13:04:22] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +130: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +98: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> +98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) +98: ResourceWarning: Enable tracemalloc to get the object allocation traceback + 91/238 Test #30: pyForceFieldConstraints ................ Passed 4.33 sec +test 133 + Start 133: pyTestGenerator + +133: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" +133: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap +133: Test timeout computed to be: 1500 +68: Test +68: +68: BMS-986142_atropBad2.mrv +68: +68: [13:04:22] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +129: [13:04:22] done +129: [13:04:22] ------------------------------------- +129: [13:04:22] Test MHFP shingling creation +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +130: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test atom-pair additional output +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test Folded Atom Pairs. +131: Randomness seeded to: 1332803486 +131: =============================================================================== +131: All tests passed (188 assertions in 16 test cases) +131: +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test Rooted Atom Pairs. +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test ignoring atoms in Atom Pairs. +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test Atom Pairs including info about chirality. +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test Morgan Fingerprints. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test morgan fp generator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator + 92/238 Test #131: fpTestCatch ............................ Passed 0.15 sec +test 134 + Start 134: pyTestMHFP + +134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" +134: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap +134: Test timeout computed to be: 1500 +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] 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 +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test Morgan Fingerprints using fromAtoms argument. +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test Morgan Fingerprints as bit vects. +121: =>start test WHIM +121: [13:04:22] test on : 365 molecules done +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [13:04:22] Explicit valence for atom # 9 N, 5, is greater than permitted +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test Morgan Fingerprints with feature invariants. + 93/238 Test #121: testWHIM ............................... Passed 2.70 sec +test 135 + Start 135: testPartialCharges + +135: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges +135: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges +135: Test timeout computed to be: 1500 +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +114: [13:04:22] ------------------------------------- +114: [13:04:22] Test empty molecule BCUT. +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test additional Morgan fingerprints options. +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Single atoms setting radius 1 bits in Morgan fingerprints +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test different invariant generator combinations +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test invariant overriding +130: [13:04:22] done +130: [13:04:22] ------------------------------------- +130: [13:04:22] Test RDKit fp generator +68: Test +68: +68: JDQ443_3d.mrv +68: +68: Test +68: +68: JDQ443_atrop1.mrv +68: +68: Test +68: +68: JDQ443_atrop2.mrv +68: +68: Test +68: +68: JDQ443_atrop3.mrv +68: +68: Test +68: +68: JDQ443_atropBad1.mrv +68: +68: [13:04:22] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +68: Test +68: +68: RP-6306_atrop1.mrv +68: +68: Test +68: +68: RP-6306_atrop2.mrv +68: +68: Test +68: +68: RP-6306_atrop3.mrv +68: +68: Test +68: +68: RP-6306_atrop4.mrv +68: +68: Test +68: +68: RP-6306_atrop5.mrv +68: +68: [13:04:22] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [13:04:22] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: Test +68: +68: RP-6306_atropBad1.mrv +68: +68: [13:04:22] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +68: Test +68: +68: RP-6306_atropBad2.mrv +68: +68: [13:04:22] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [13:04:22] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [13:04:22] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +129: [13:04:22] done +129: [13:04:22] ------------------------------------- +129: [13:04:22] Test MHFP hashing of string and uint arrays +129: [13:04:22] done +129: [13:04:22] ------------------------------------- +129: [13:04:22] Test SECFP fingerprint functionality +129: [13:04:22] done +112: [13:04:22] done +112: [13:04:22] ------------------------------------- +112: [13:04:22] Test Github #3806: NaNs from AUTOCORR2D descriptor +112: [13:04:22] done +116: [13:04:22] done +98: ..[13:04:22] == testRGroupState +98: .[13:04:22] == testRandomEnumerateAllBBsLibrary +98: ** [1, 1] +98: ** [0, 2] +98: ** [1, 0] +97: ...[13:04:22] 97: 97: **** 97: Pre-condition Violation @@ -22999,7 +24286,7 @@ 97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202503.1/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-202503.1/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# 0x00007EFDB5F6062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x00007FB1D94DC62C 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-202503.1/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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -23010,17 +24297,17 @@ 97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-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-202503.1/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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x00007EFDB3BB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x00007EFDB3BB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x00007EFDB3BB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x00007EFDB3BB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x00007EFDB3BB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x00007FB1D71B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x00007FB1D71B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x00007FB1D71B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x00007FB1D71B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x00007FB1D71B7933 in /build/reproducible-path/rdkit-202503.1/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-202503.1/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-202503.1/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-202503.1/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-202503.1/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# 0x00007EFDB5F5D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x00007FB1D94D93C6 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# 0x00000000005CBA19 in /usr/bin/python3 @@ -23052,15 +24339,61 @@ 97: 75# 0x00000000006B339E in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x00007EFDB696FCA8 in /lib/x86_64-linux-gnu/libc.so.6 +97: 78# 0x00007FB1D9EEBCA8 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: [03:35:37] +132: Randomness seeded to: 3631343572 +132: =============================================================================== +132: All tests passed (2737 assertions in 7 test cases) +132: + 94/238 Test #99: pyChemReactionSanitize ................. Passed 3.65 sec + 95/238 Test #112: testAUTOCORR2D ......................... Passed 3.39 sec + 96/238 Test #114: testBCUT ............................... Passed 3.32 sec + 97/238 Test #116: testPBF ................................ Passed 3.24 sec + 98/238 Test #129: testMHFPFingerprint .................... Passed 0.36 sec + 99/238 Test #135: testPartialCharges ..................... Passed 0.14 sec +97: [13:04:22] 97: 97: **** +test 136 + Start 136: pyPartialCharges + +136: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" +136: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap +136: Test timeout computed to be: 1500 +test 137 + Start 137: testMolTransforms + +137: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms +137: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms +137: Test timeout computed to be: 1500 +test 138 + Start 138: molTransformsTestCatch + +138: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch +138: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms +138: Test timeout computed to be: 1500 +test 139 + Start 139: pyMolTransforms + +139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" +139: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap +139: Test timeout computed to be: 1500 +test 140 + Start 140: forceFieldHelpersCatch + +140: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch +140: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers +140: Test timeout computed to be: 1500 +test 141 + Start 141: testMMFFForceFieldHelpers + +141: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers +141: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF +141: Test timeout computed to be: 1500 97: Pre-condition Violation 97: getNumImplicitHs() called without preceding call to calcImplicitValence() 97: Violation occurred on line 301 in file ./Code/GraphMol/Atom.cpp @@ -23092,7 +24425,7 @@ 97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202503.1/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-202503.1/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# 0x00007EFDB5F6062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x00007FB1D94DC62C 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-202503.1/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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -23103,17 +24436,17 @@ 97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-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-202503.1/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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x00007EFDB3BB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x00007EFDB3BB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x00007EFDB3BB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x00007EFDB3BB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x00007EFDB3BB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x00007FB1D71B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x00007FB1D71B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x00007FB1D71B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x00007FB1D71B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x00007FB1D71B7933 in /build/reproducible-path/rdkit-202503.1/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-202503.1/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-202503.1/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-202503.1/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-202503.1/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# 0x00007EFDB5F5D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x00007FB1D94D93C6 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# 0x00000000005CBA19 in /usr/bin/python3 @@ -23145,403 +24478,52 @@ 97: 75# 0x00000000006B339E in /usr/bin/python3 97: 76# Py_RunMain in /usr/bin/python3 97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x00007EFDB696FCA8 in /lib/x86_64-linux-gnu/libc.so.6 +97: 78# 0x00007FB1D9EEBCA8 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: -68: Test -68: -68: marvin03.mrv -68: -68: Test -68: -68: Cubane.mrv -68: -68: Test -68: -68: FalseAtropisomer.mrv -68: -68: Test -68: -68: AtropEnhancedStereo.mrv -68: -68: Test -68: -68: AtropManyChirals.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced2.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced3.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced4.mrv -68: -68: Test -68: -68: BMS-986142_3d_chiral.mrv -68: -68: Test -68: -68: BMS-986142_3d.mrv -68: -68: Test -68: -68: BMS-986142_atrop1.mrv -68: -68: Test -68: -68: BMS-986142_atrop2.mrv -68: -68: Test -68: -68: BMS-986142_atrop3.mrv -68: -68: Test -68: -68: BMS-986142_atrop4.mrv -68: -68: Test -68: -68: BMS-986142_atrop5.mrv -68: -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: Test -68: -68: BMS-986142_atrop6.mrv -68: -68: Test -68: -68: BMS-986142_atrop7.mrv -68: -68: Test -68: -68: BMS-986142_atrop8.mrv -68: -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: Test -68: -68: BMS-986142_atropBad2.mrv -68: -68: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: .........[03:35:37] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [03:35:37] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [03:35:37] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [03:35:37] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: .[03:35:37] product atom-mapping number 1 found multiple times. -97: [03:35:37] product atom-mapping number 1 found multiple times. -98: ..[03:35:37] == testRGroupState -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: [03:35:37] done -111: [03:35:37] ------------------------------------- -111: [03:35:37] Test VSA descriptors. -111: [03:35:37] done -111: [03:35:37] ------------------------------------- -111: [03:35:37] Test molecular formula calculation. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -111: [03:35:37] done -111: [03:35:37] ------------------------------------- -111: [03:35:37] Test Issue 3415534. -111: [03:35:37] done -111: [03:35:37] ------------------------------------- -111: [03:35:37] Test Issue3433771: Bad definition for Crippen atom type O11. -111: [03:35:37] done -111: [03:35:37] ------------------------------------- -111: [03:35:37] Test multithreading -111: reading molecules -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 84/238 Test #99: pyChemReactionSanitize ................. Passed 0.37 sec -98: .[03:35:37] == testRandomEnumerateAllBBsLibrary -test 124 - Start 124: testCoulombMat - -124: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat -124: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -124: Test timeout computed to be: 1500 -98: ** [1, 1] -98: ** [0, 2] -98: ** [1, 0] -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] 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. - 85/238 Test #107: filterCatalogTest ...................... Passed 0.34 sec -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 125 - Start 125: descriptorsTestCatch - -125: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch -125: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -125: Test timeout computed to be: 1500 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: JDQ443_3d.mrv -68: -68: Test -68: -68: JDQ443_atrop1.mrv -68: -68: Test -68: -68: JDQ443_atrop2.mrv -68: -68: Test -68: -68: JDQ443_atrop3.mrv -68: -68: Test -68: -68: JDQ443_atropBad1.mrv -68: -68: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[03:35:37] == testRandomEnumerateLibrary -97: ................[03:35:37] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [03:35:37] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: done -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [03:35:37] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: [03:35:37] done -90: [03:35:37] ------------------------------------- -90: [03:35:37] Test GitHub issue 15 -90: [03:35:37] done -90: [03:35:37] ------------------------------------- -90: [03:35:37] Test GitHub issue 409 -91: Randomness seeded to: 3467765177 -91: =============================================================================== -91: All tests passed (242 assertions in 12 test cases) -91: -90: [03:35:37] done -90: [03:35:37] ------------------------------------- -90: [03:35:37] Test chiral matching -97: ..[03:35:37] reactant 2 has no mapped atoms. -97: [03:35:37] reactant 2 has no mapped atoms. -97: [03:35:37] product 1 has no mapped atoms. -68: Test -68: -68: RP-6306_atrop1.mrv -68: -68: Test -68: -68: RP-6306_atrop2.mrv -68: -68: Test -68: -68: RP-6306_atrop3.mrv -68: -68: Test -68: -68: RP-6306_atrop4.mrv -68: -68: Test -68: -68: RP-6306_atrop5.mrv -68: -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: Test -68: -68: RP-6306_atropBad1.mrv -68: -68: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -90: [03:35:37] done -90: [03:35:37] ------------------------------------- -90: [03:35:37] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -90: [03:35:37] done -90: [03:35:37] ------------------------------------- -90: [03:35:37] Test dative-bond matching -90: [03:35:37] done -90: [03:35:37] ------------------------------------- -90: [03:35:37] Test cis/trans matching -90: [03:35:37] done -90: [03:35:37] ------------------------------------- -90: [03:35:37] Test cis/trans matching part 2 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -98: .[03:35:37] == testRandomSample -111: processing -111: launch :0 -111: launch :1 - 86/238 Test #91: substructTestCatch ..................... Passed 0.43 sec - 87/238 Test #103: pyTautomerQuery ........................ Passed 0.38 sec -111: launch :2 -111: launch :3 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: [03:35:37] done -90: [03:35:37] ------------------------------------- -90: [03:35:37] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -test 126 - Start 126: pyMolDescriptors - -126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" -126: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap -126: Test timeout computed to be: 1500 -test 127 - Start 127: pyMolDescriptors3D - -127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Descriptors/Wrap/test3D.py" -127: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap -127: Test timeout computed to be: 1500 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: [03:35:37] done -97: ........[03:35:37] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -97: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -97: [03:35:37] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -97: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -97: .[03:35:37] reactant atom-mapping number 1 found multiple times. -97: [03:35:37] product atom-mapping number 2 not found in reactants. -97: [03:35:37] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 4 -97: [03:35:37] product atom-mapping number 5 not found in reactants. -98: .[03:35:37] == testRandomSampleAllBBs -98: .[03:35:37] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: [03:35:37] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: .[03:35:37] == testRemoveBadMatches -98: .[03:35:37] == testTimings -68: Test -68: -68: RP-6306_atropBad2.mrv -68: -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: [03:35:37] ------------------------------------- -90: [03:35:37] Testing matching E/Z against Cis/Trans stereo bonds -124: ===================== Testing CoulombMat ======================= -116: [03:35:37] done -116: [03:35:37] ------------------------------------- -116: [03:35:37] PBF edge cases. -116: [03:35:37] done -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: [03:35:37] -90: -90: **** - 88/238 Test #116: testPBF ................................ Passed 0.30 sec -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 128 - Start 128: testFingerprints - -128: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints -128: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -128: Test timeout computed to be: 1500 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -90: Pre-condition Violation -90: matches must not be empty -90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -90: Failed Expression: !matches.empty() -90: ---------- -90: Stacktrace: -90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/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-202503.1/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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x000055A64346D37A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x000055A64345DBE1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x00007F4661C33CA8 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# 0x000055A64345DD21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: ---------- -90: **** -90: -90: [03:35:37] -90: -90: **** -90: Pre-condition Violation -90: matches must not be empty -90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -90: Failed Expression: !matches.empty() -90: ---------- -90: Stacktrace: -90: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/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-202503.1/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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x000055A643458423 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x000055A64345DBE1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x00007F4661C33CA8 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# 0x000055A64345DD21 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: ---------- -90: **** -90: -90: [03:35:37] ------------------------------------- -90: [03:35:37] Test substructure matching with a pathological case for symmetric SSSR -90: [03:35:37] ------------------------------------- -90: [03:35:37] Test isAtomTerminalRGroupOrQueryHydrogen - 89/238 Test #90: testSubstructMatch ..................... Passed 0.45 sec -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 129 - Start 129: testMHFPFingerprint - -129: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint -129: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -129: Test timeout computed to be: 1500 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 200 -115: [03:35:37] 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 - 90/238 Test #124: testCoulombMat ......................... Passed 0.06 sec -test 130 - Start 130: testFingerprintGenerators - -130: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators -130: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -130: Test timeout computed to be: 1500 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +93: [13:04:22] reactant 0 has no mapped atoms. +93: [13:04:22] product 0 has no mapped atoms. +93: [13:04:22] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [13:04:22] Explicit valence for atom # 3 Al, 6, is greater than permitted +110: ......... +110: ---------------------------------------------------------------------- +110: Ran 9 tests in 0.301s +110: +110: OK 68: Test 68: 68: RP-6306_3d.mrv @@ -23566,1329 +24548,138 @@ 68: 68: Sotorasib_atrop5.mrv 68: -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [13:04:22] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [13:04:22] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 68: Test 68: 68: Sotorasib_atropBad1.mrv 68: -68: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: Sotorasib_atropBad2.mrv -68: -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] 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-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> -97: png = open(fname, 'rb').read() -97: ResourceWarning: Enable tracemalloc to get the object allocation traceback -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 34 -97: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 36 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 38 -97: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 40 -97: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 42 -97: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 87 -97: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 89 -97: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 91 -97: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 93 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [03:35:37] Found a SCD/SED line with missing/empty SDT specification at line 95 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -129: [03:35:37] ------------------------------------- -129: [03:35:37] Test MHFP fingerprint encoder initialization -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [03:35:37] done -112: [03:35:37] ------------------------------------- -112: [03:35:37] Test Github #3806: NaNs from AUTOCORR2D descriptor -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [03:35:37] done - 91/238 Test #112: testAUTOCORR2D ......................... Passed 0.38 sec -test 131 - Start 131: fpTestCatch - -131: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch -131: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -131: Test timeout computed to be: 1500 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: ..[03:35:37] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [03:35:37] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test atom-pair fp generator -97: [03:35:37] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [03:35:37] reaction has no reactants -97: [03:35:37] reaction has no products -97: [03:35:37] initialization failed -97: [03:35:37] reaction has no reactants -97: [03:35:37] reaction has no products -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: Sotorasib_3d.mrv -68: -68: Test -68: -68: ZM374979_atrop1.mrv -68: -68: Test -68: -68: ZM374979_atrop2.mrv -68: -68: Test -68: -68: ZM374979_atrop3.mrv -68: -68: Test -68: -68: ZM374979_atropBad1.mrv -68: -68: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -120: [03:35:37] done -120: [03:35:37] ------------------------------------- -120: [03:35:37] More PMI/NPR tests. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -120: [03:35:37] done -120: [03:35:37] ------------------------------------- -120: [03:35:37] Basic NPR tests. -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: Atoms: -128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: 1 conj?: 1 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -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: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: 1 conj?: 1 -128: 9 8->10 order: a conj?: 1 aromatic?: 1 -128: 10 10->1 order: a conj?: 1 aromatic?: 1 -128: 11 7->3 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -97: .[03:35:37] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -97: [03:35:37] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [03:35:37] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [03:35:37] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [03:35:37] reaction has no reactants -97: [03:35:37] reaction has no products -97: [03:35:37] initialization failed -97: [03:35:37] reaction has no reactants -97: [03:35:37] reaction has no products -97: . -97: ---------------------------------------------------------------------- -97: Ran 54 tests in 0.160s -97: -97: OK -97: ******************************************** -97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -97: -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -125: Randomness seeded to: 1140945997 -125: Warning: Atom Count for residue GLU5A does not match expected count -125: Warning: Atom Count for residue ASN39A does not match expected count -128: SMI: Oc1cc2[nH]cnc2c(O)n1 -128: Atoms: -128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: 1 conj?: 1 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -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: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: 1 conj?: 1 -128: 9 8->10 order: a conj?: 1 aromatic?: 1 -128: 10 10->1 order: a conj?: 1 aromatic?: 1 -128: 11 7->3 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: c1(O)cc2[nH]cnc2c(O)n1 -128: Atoms: -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 -128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: 1 conj?: 1 -128: 1 0->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -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: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: 1 conj?: 1 -128: 9 8->10 order: a conj?: 1 aromatic?: 1 -128: 10 10->0 order: a conj?: 1 aromatic?: 1 -128: 11 7->3 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: c1c(O)nc(O)c2c1[nH]cn2 -128: Atoms: -128: 0 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 3 7 N chg: 0 deg: 2 exp: 3 imp: 0 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 -128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 7 6 C chg: 0 deg: 3 exp: 4 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 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: a conj?: 1 aromatic?: 1 -128: 1 1->2 order: 1 conj?: 1 -128: 2 1->3 order: a conj?: 1 aromatic?: 1 -128: 3 3->4 order: a conj?: 1 aromatic?: 1 -128: 4 4->5 order: 1 conj?: 1 -128: 5 4->6 order: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: a conj?: 1 aromatic?: 1 -128: 9 9->10 order: a conj?: 1 aromatic?: 1 -128: 10 7->0 order: a conj?: 1 aromatic?: 1 -128: 11 10->6 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: -128: SMI: c12cc(O)nc(O)c1nc[nH]2 -128: Atoms: -128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 3 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -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 -128: 7 6 C chg: 0 deg: 3 exp: 4 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 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: a conj?: 1 aromatic?: 1 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: 1 conj?: 1 -128: 3 2->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 -128: 6 5->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: a conj?: 1 aromatic?: 1 -128: 9 9->10 order: a conj?: 1 aromatic?: 1 -128: 10 7->0 order: a conj?: 1 aromatic?: 1 -128: 11 10->0 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: SMI: [nH]1c2cc(O)nc(O)c2nc1 -128: Atoms: -128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -125: Warning: Atom Count for residue GLU53A does not match expected count -128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -130: [03:35:37] done -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test atom-pair fp generator with different arguments -128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -130: [03:35:37] done -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -128: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -130: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -125: Warning: Atom Count for residue ARG64A does not match expected count -128: 9 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -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 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -130: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: 3 3->4 order: 1 conj?: 1 -128: 4 3->5 order: a conj?: 1 aromatic?: 1 -128: 5 5->6 order: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: 1 conj?: 1 -128: 7 6->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: a conj?: 1 aromatic?: 1 -128: 9 9->10 order: a conj?: 1 aromatic?: 1 -128: 10 10->0 order: a conj?: 1 aromatic?: 1 -128: 11 8->1 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -130: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: SMI: c1[nH]c2cc(O)nc(O)c2n1 -130: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: Atoms: -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 -130: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [03:35:37] 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: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -125: Warning: Atom Count for residue LYS80A does not match expected count -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 -130: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 8 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: a conj?: 1 aromatic?: 1 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -128: 3 3->4 order: a conj?: 1 aromatic?: 1 -128: 4 4->5 order: 1 conj?: 1 -128: 5 4->6 order: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: 1 conj?: 1 -128: 8 7->9 order: a conj?: 1 aromatic?: 1 -128: 9 9->10 order: a conj?: 1 aromatic?: 1 -128: 10 10->0 order: a conj?: 1 aromatic?: 1 -128: 11 9->2 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: SMI: n1c[nH]c2cc(O)nc(O)c21 -128: Atoms: -128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -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 -128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 9 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 10 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: a conj?: 1 aromatic?: 1 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -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 -128: 6 5->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: 1 conj?: 1 -128: 9 8->10 order: a conj?: 1 aromatic?: 1 -128: 10 10->0 order: a conj?: 1 aromatic?: 1 -128: 11 10->3 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: c12c(cc(O)nc1O)[nH]cn2 -128: Atoms: -128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 2 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -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 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: a conj?: 1 aromatic?: 1 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -128: 3 3->4 order: 1 conj?: 1 -128: 4 3->5 order: a conj?: 1 aromatic?: 1 -128: 5 5->6 order: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: 1 conj?: 1 -128: 7 1->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: a conj?: 1 aromatic?: 1 -128: 9 9->10 order: a conj?: 1 aromatic?: 1 -128: 10 6->0 order: a conj?: 1 aromatic?: 1 -128: 11 10->0 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: c1(O)c2c(cc(O)n1)[nH]cn2 -128: Atoms: -128: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 1 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -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 -128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -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 -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 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: 1 conj?: 1 -128: 1 0->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -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 -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 -128: 9 9->10 order: a conj?: 1 aromatic?: 1 -128: 10 7->0 order: a conj?: 1 aromatic?: 1 -128: 11 10->2 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: Oc1c2c(cc(O)n1)[nH]cn2 -128: Atoms: -128: 0 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -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 -128: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -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 -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 -128: 10 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: Bonds: -128: 0 0->1 order: 1 conj?: 1 -128: 1 1->2 order: a conj?: 1 aromatic?: 1 -128: 2 2->3 order: a conj?: 1 aromatic?: 1 -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 -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 -128: 9 9->10 order: a conj?: 1 aromatic?: 1 -128: 10 7->1 order: a conj?: 1 aromatic?: 1 -128: 11 10->2 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: SMI: n1c(O)cc2[nH]cnc2c1O -128: Atoms: -128: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 2 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -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 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 6 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: SP2 arom?: 1 -128: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: SP2 arom?: 1 -128: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: SP2 arom?: 1 -128: 10 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: SP2 -128: Bonds: -128: 0 0->1 order: a conj?: 1 aromatic?: 1 -128: 1 1->2 order: 1 conj?: 1 -128: 2 1->3 order: a conj?: 1 aromatic?: 1 -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: a conj?: 1 aromatic?: 1 -128: 6 6->7 order: a conj?: 1 aromatic?: 1 -128: 7 7->8 order: a conj?: 1 aromatic?: 1 -128: 8 8->9 order: a conj?: 1 aromatic?: 1 -128: 9 9->10 order: 1 conj?: 1 -128: 10 9->0 order: a conj?: 1 aromatic?: 1 -128: 11 8->4 order: a conj?: 1 aromatic?: 1 -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -130: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -67: ..............[03:35:37] SMILES Parse Error: syntax error while parsing: invalidsmiles -67: [03:35:37] SMILES Parse Error: check for mistakes around position 1: -67: [03:35:37] invalidsmiles -67: [03:35:37] ^ -67: [03:35:37] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -128: -128: -128: -128: -128: -128: -128: -128: -128: ------------------- -128: -130: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -125: Warning: Atom Count for residue GLU150A does not match expected count -125: Warning: Atom Count for residue ASN157A does not match expected count -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -129: [03:35:37] done -129: [03:35:37] ------------------------------------- -129: [03:35:37] Test MHFP shingling creation -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -68: Test -68: -68: mrtx1719_3d.mrv -68: -68: Test -68: -68: mrtx1719_atrop1.mrv -68: -68: Test -68: -68: mrtx1719_atrop2.mrv -68: -68: Test -68: -68: mrtx1719_atrop3.mrv -68: -68: Test -68: -68: mrtx1719_atropBad1.mrv -68: -68: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -130: [03:35:37] done -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test atom-pair additional output -130: [03:35:37] done -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test Folded Atom Pairs. -130: [03:35:37] done -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test Rooted Atom Pairs. -130: [03:35:37] done -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test ignoring atoms in Atom Pairs. -130: [03:35:37] done -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test Atom Pairs including info about chirality. -130: [03:35:37] done -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test Morgan Fingerprints. -130: [03:35:37] done -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test morgan fp generator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test Morgan Fingerprints. -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test Morgan Fingerprints using fromAtoms argument. -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test Morgan Fingerprints as bit vects. -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test Morgan Fingerprints with feature invariants. -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test additional Morgan fingerprints options. -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test Atom Codes. -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test Atom Pairs. -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test Atom Pairs part 2. -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test Topological Torsions. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test Bulk Topological Torsions. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:37] done -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test Morgan Fingerprints using fromAtoms argument. -130: [03:35:37] done -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test Morgan Fingerprints as bit vects. -130: [03:35:37] done -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test Morgan Fingerprints with feature invariants. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:37] done -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test additional Morgan fingerprints options. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:37] done -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -130: [03:35:37] done -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:37] ------------------------------------- -130: [03:35:37] Single atoms setting radius 1 bits in Morgan fingerprints -130: [03:35:37] done -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test different invariant generator combinations -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:37] done -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test invariant overriding -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:37] done -130: [03:35:37] ------------------------------------- -130: [03:35:37] Test RDKit fp generator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] 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 0.599s -30: -30: OK -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -93: [03:35:37] reactant 0 has no mapped atoms. -93: [03:35:37] product 0 has no mapped atoms. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -131: Randomness seeded to: 3025973885 -131: =============================================================================== -131: All tests passed (188 assertions in 16 test cases) -131: -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator - 92/238 Test #131: fpTestCatch ............................ Passed 0.07 sec -test 132 - Start 132: fpGenTestCatch - -132: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch -132: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -132: Test timeout computed to be: 1500 -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -93: [03:35:37] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -129: [03:35:37] done -129: [03:35:37] ------------------------------------- -129: [03:35:37] Test MHFP hashing of string and uint arrays -129: [03:35:37] done -129: [03:35:37] ------------------------------------- -129: [03:35:37] Test SECFP fingerprint functionality -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator - 93/238 Test #93: testReaction ........................... Passed 0.59 sec -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -test 133 - Start 133: pyTestGenerator - -133: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" -133: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap -133: Test timeout computed to be: 1500 -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 300 -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: FalseAtropisomer.mrv -68: -68: Test -68: -68: AtropEnhancedStereo.mrv -68: -68: Test -68: -68: AtropManyChirals.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced2.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced3.mrv -68: -68: Test -68: -68: AtropManyChiralsEnhanced4.mrv -68: -68: Test -68: -68: BMS-986142_3d_chiral.mrv -68: -68: Test -68: -68: BMS-986142_3d.mrv -68: -68: Test -68: -68: BMS-986142_atrop1.mrv -68: -68: Test -68: -68: BMS-986142_atrop2.mrv -68: -68: Test -68: -68: BMS-986142_atrop3.mrv -68: -68: Test -68: -68: BMS-986142_atrop4.mrv -68: -68: Test -68: -68: BMS-986142_atrop5.mrv -68: -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -92: Randomness seeded to: 2636521617 -92: =============================================================================== -92: All tests passed (11480 assertions in 38 test cases) -92: - 94/238 Test #30: pyForceFieldConstraints ................ Passed 0.86 sec -test 134 - Start 134: pyTestMHFP +68: [13:04:22] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +98: .[13:04:22] == testRandomEnumerateLibrary +123: =>start test autocorr3D +123: [13:04:22] test on : 365 molecules done +100/238 Test #93: testReaction ........................... Passed 3.77 sec +101/238 Test #132: fpGenTestCatch ......................... Passed 0.35 sec +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 142 + Start 142: testMMFFForceFieldHelpersMultiThread -134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" -134: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap -134: Test timeout computed to be: 1500 -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 95/238 Test #92: testGenericGroups ...................... Passed 0.61 sec -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 135 - Start 135: testPartialCharges +142: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread +142: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF +142: Test timeout computed to be: 1500 +test 143 + Start 143: testUFFForceFieldHelpers -135: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges -135: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges -135: Test timeout computed to be: 1500 -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -129: [03:35:37] done -68: Test -68: -68: BMS-986142_atrop6.mrv -68: -68: Test -68: -68: BMS-986142_atrop7.mrv -68: +143: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers +143: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF +143: Test timeout computed to be: 1500 +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: BMS-986142_atrop8.mrv +68: Sotorasib_atropBad2.mrv 68: -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -125: Warning: Atom Count for residue GLU5A does not match expected count - 96/238 Test #129: testMHFPFingerprint .................... Passed 0.17 sec -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -test 136 - Start 136: pyPartialCharges +68: [13:04:22] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +102/238 Test #123: testAUTOCORR3D ......................... Passed 2.87 sec +test 144 + Start 144: testCrystalForceField -136: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" -136: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap -136: Test timeout computed to be: 1500 -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: Test -68: -68: BMS-986142_atropBad2.mrv -68: -68: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 97/238 Test #97: pyChemReactions ........................ Passed 0.61 sec -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 137 - Start 137: testMolTransforms +144: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField +144: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF +144: Test timeout computed to be: 1500 +97: .........[13:04:22] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [13:04:22] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [13:04:22] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [13:04:22] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: .[13:04:22] product atom-mapping number 1 found multiple times. +97: [13:04:22] product atom-mapping number 1 found multiple times. +98: .[13:04:22] == testRandomSample +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +120: [13:04:22] done +120: [13:04:22] ------------------------------------- +120: [13:04:22] More PMI/NPR tests. +120: [13:04:22] done +120: [13:04:22] ------------------------------------- +120: [13:04:22] Basic NPR tests. +89: [13:04:22] Explicit valence for atom # 4 Al, 6, is greater than permitted +98: .[13:04:22] == testRandomSampleAllBBs +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [13:04:22] ------------------------------------- +141: [13:04:22] Test MMFF atom types. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +144: ------------------------------------- +144: Test CrystalFF torsional term. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +138: Randomness seeded to: 20971397 +138: =============================================================================== +138: All tests passed (4 assertions in 1 test case) +138: +103/238 Test #138: molTransformsTestCatch ................. Passed 0.11 sec +test 145 + Start 145: pyForceFieldHelpers -137: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms -137: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms -137: Test timeout computed to be: 1500 -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -89: [03:35:37] Explicit valence for atom # 9 N, 5, is greater than permitted -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -68: Test -68: -68: JDQ443_3d.mrv -68: -68: Test -68: -68: JDQ443_atrop1.mrv -68: -68: Test -68: -68: JDQ443_atrop2.mrv -68: -68: Test -68: -68: JDQ443_atrop3.mrv -68: -68: Test -68: -68: JDQ443_atropBad1.mrv -68: -68: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test Hashed Atom Pairs. -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test Hashed torsions. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test Rooted Atom Pairs. -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test ignoring atoms in Atom Pairs. -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test Rooted Topological Torsions. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test ignoring atoms in Topological Torsions. -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test atom info from morgan fingerprints. -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] Test atom info from morgan fingerprints including Info Redundant Environments. -115: [03:35:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:37] done -128: [03:35:37] ------------------------------------- -128: [03:35:37] ------------------------------------- -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:37] DEPRECATION WARNING: please use AtomPairGenerator -121: =>start test WHIM -121: [03:35:37] test on : 365 molecules done -68: Test -68: -68: RP-6306_atrop1.mrv -68: -68: Test -68: -68: RP-6306_atrop2.mrv -68: -68: Test -68: -68: RP-6306_atrop3.mrv -68: -68: Test -68: -68: RP-6306_atrop4.mrv -68: -68: Test -68: -68: RP-6306_atrop5.mrv -68: -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:37] ------------------------------------- -68: Test -68: -68: RP-6306_atropBad1.mrv -68: -68: [03:35:37] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -68: Test -68: -68: RP-6306_atropBad2.mrv -68: -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [03:35:37] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -68: [03:35:37] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +145: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" +145: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap +145: Test timeout computed to be: 1500 +98: .[13:04:22] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: [13:04:22] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: .[13:04:22] == testRemoveBadMatches +98: .[13:04:22] == testTimings +89: [13:04:22] Explicit valence for atom # 10 Si, 6, is greater than permitted +142: [13:04:22] ------------------------------------- +142: [13:04:22] Test MMFF multithreading +143: [13:04:22] ------------------------------------- +143: [13:04:22] Test UFF atom labels. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +140: Randomness seeded to: 2184554475 +140: =============================================================================== +140: All tests passed (17 assertions in 2 test cases) +140: 137: *********************************************************** 137: Testing MolTransforms 137: --------------------------------- @@ -24919,53 +24710,32 @@ 137: testWeightedCentroid 137: 137: *********************************************************** - 98/238 Test #137: testMolTransforms ...................... Passed 0.06 sec -test 138 - Start 138: molTransformsTestCatch +141: [13:04:22] done +141: [13:04:22] ------------------------------------- +141: [13:04:22] Testing MMFF builder tools. +104/238 Test #137: testMolTransforms ...................... Passed 0.15 sec +test 146 + Start 146: testDistGeomHelpers -138: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch -138: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms -138: Test timeout computed to be: 1500 -117: =>start test rdf custom -117: [03:35:38] test on : 365 molecules done -68: Test -68: -68: RP-6306_3d.mrv -68: -68: Test -68: -68: Sotorasib_atrop1.mrv -68: -68: Test -68: -68: Sotorasib_atrop2.mrv -68: -68: Test -68: -68: Sotorasib_atrop3.mrv -68: -68: Test -68: -68: Sotorasib_atrop4.mrv -68: -68: Test -68: -68: Sotorasib_atrop5.mrv -68: -68: [03:35:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: [03:35:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: Test -68: -68: Sotorasib_atropBad1.mrv -68: -68: [03:35:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -68: Test -68: -68: Sotorasib_atropBad2.mrv -68: -68: [03:35:38] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -114: [03:35:38] ------------------------------------- -114: [03:35:38] Test empty molecule BCUT. +146: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers +146: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers +146: Test timeout computed to be: 1500 +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +105/238 Test #140: forceFieldHelpersCatch ................. Passed 0.13 sec +test 147 + Start 147: distGeomHelpersCatch + +147: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch +147: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers +147: Test timeout computed to be: 1500 +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +143: [13:04:22] done +143: [13:04:22] ------------------------------------- +143: [13:04:22] Test UFF atom typer. 68: Test 68: 68: Sotorasib_3d.mrv @@ -24986,223 +24756,137 @@ 68: 68: ZM374979_atropBad1.mrv 68: -68: [03:35:38] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -118: =>start test rdf -118: [03:35:38] test on : 365 molecules done -120: [03:35:38] done -120: [03:35:38] ------------------------------------- -120: [03:35:38] PMI edge cases. -120: [03:35:38] done -120: [03:35:38] ------------------------------------- -120: [03:35:38] NPR edge cases. -120: [03:35:38] done -120: [03:35:38] ------------------------------------- -120: [03:35:38] 3D descriptors. -120: [03:35:38] done -120: [03:35:38] ------------------------------------- -120: [03:35:38] 3D descriptor edge cases. -120: [03:35:38] done -120: [03:35:38] ------------------------------------- -120: [03:35:38] Inertial shape factor. -120: [03:35:38] done -123: =>start test autocorr3D -123: [03:35:38] test on : 365 molecules done -109: [03:35:38] -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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x00007F3B85739DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x000055EB66E501FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x000055EB66E4D6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007F3B84A33CA8 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# 0x000055EB66E4D7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: ---------- -109: **** -109: -109: [03:35:38] -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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x00007F3B85739DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x000055EB66E501FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x000055EB66E4D6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007F3B84A33CA8 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# 0x000055EB66E4D7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: ---------- -109: **** -109: -109: [03:35:38] -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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x00007F3B85739DFD in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x000055EB66E501FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x000055EB66E4D6A1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x00007F3B84A33CA8 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# 0x000055EB66E4D7D1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: ---------- -109: **** -109: - 99/238 Test #114: testBCUT ............................... Passed 2.13 sec -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:39] ------------------------------------- -128: [03:35:39] ------------------------------------- -test 139 - Start 139: pyMolTransforms - -139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" -139: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap -139: Test timeout computed to be: 1500 -100/238 Test #109: testFragCatalog ........................ Passed 2.18 sec -101/238 Test #121: testWHIM ............................... Passed 1.97 sec -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:39] ------------------------------------- -128: [03:35:39] Test Atom Pairs including info about chirality. -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] done -128: [03:35:39] ------------------------------------- -128: [03:35:39] Test Topological Torsions including info about chirality. -128: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:39] done -128: [03:35:39] ------------------------------------- -128: [03:35:39] Test GitHub Issue 25: fingerprint backwards compatibility. -128: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] done -128: [03:35:39] ------------------------------------- -128: [03:35:39] Test GitHub Issue 151: PatternFingerprint problems -test 140 - Start 140: forceFieldHelpersCatch - -140: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch -140: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers -140: Test timeout computed to be: 1500 -test 141 - Start 141: testMMFFForceFieldHelpers - -141: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers -141: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF -141: Test timeout computed to be: 1500 -102/238 Test #118: testRDF ................................ Passed 2.10 sec -103/238 Test #135: testPartialCharges ..................... Passed 1.66 sec -104/238 Test #123: testAUTOCORR3D ......................... Passed 1.90 sec -110: ......... -110: ---------------------------------------------------------------------- -110: Ran 9 tests in 1.651s -110: -110: OK -105/238 Test #120: test3D ................................. Passed 2.05 sec -119: =>start test MORSE -119: =>read file -119: [03:35:39] test on : 365 molecules done -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [03:35:39] done -128: [03:35:39] ------------------------------------- -128: [03:35:39] Test 3D atom pairs. -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:39] done -128: [03:35:39] ------------------------------------- -128: [03:35:39] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -128: [03:35:39] done -128: [03:35:39] ------------------------------------- -128: [03:35:39] Test multithreading with the pattern FP -128: reading molecules -test 142 - Start 142: testMMFFForceFieldHelpersMultiThread - -142: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread -142: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF -142: Test timeout computed to be: 1500 -test 143 - Start 143: testUFFForceFieldHelpers - -143: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers -143: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF -143: Test timeout computed to be: 1500 -test 144 - Start 144: testCrystalForceField - -144: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField -144: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF -144: Test timeout computed to be: 1500 -test 145 - Start 145: pyForceFieldHelpers - -145: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" -145: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap -145: Test timeout computed to be: 1500 -138: Randomness seeded to: 96678946 -138: =============================================================================== -138: All tests passed (4 assertions in 1 test case) -138: +68: [13:04:22] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +143: [13:04:22] done +143: [13:04:22] ------------------------------------- +143: [13:04:22] Testing UFF builder tools. +143: [13:04:22] done +143: [13:04:22] ------------------------------------- +143: [13:04:22] Testing UFF builder+minimization. +141: [13:04:22] done +141: [13:04:22] ------------------------------------- +141: [13:04:22] Testing MMFF builder+minimization. +97: ................[13:04:22] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: [13:04:22] 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. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 300 +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +97: [13:04:22] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +97: ..[13:04:22] reactant 2 has no mapped atoms. +97: [13:04:22] reactant 2 has no mapped atoms. +97: [13:04:22] product 1 has no mapped atoms. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test Hashed Atom Pairs. +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test Hashed torsions. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test Rooted Atom Pairs. +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test ignoring atoms in Atom Pairs. +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test Rooted Topological Torsions. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test ignoring atoms in Topological Torsions. +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:22] done +128: [13:04:22] ------------------------------------- +128: [13:04:22] Test atom info from morgan fingerprints. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:23] done +128: [13:04:23] ------------------------------------- +128: [13:04:23] Test atom info from morgan fingerprints including Info Redundant Environments. +128: [13:04:23] done +128: [13:04:23] ------------------------------------- +128: [13:04:23] ------------------------------------- +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator 68: Test 68: 68: mrtx1719_3d.mrv @@ -25223,522 +24907,667 @@ 68: 68: mrtx1719_atropBad1.mrv 68: -68: [03:35:39] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -106/238 Test #119: testMORSE .............................. Passed 2.12 sec -107/238 Test #138: molTransformsTestCatch ................. Passed 1.59 sec -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 146 - Start 146: testDistGeomHelpers - -146: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers -146: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers -146: Test timeout computed to be: 1500 -test 147 - Start 147: distGeomHelpersCatch - -147: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch -147: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers -147: Test timeout computed to be: 1500 -132: Randomness seeded to: 2184169327 -132: =============================================================================== -132: All tests passed (2737 assertions in 7 test cases) -132: -108/238 Test #132: fpGenTestCatch ......................... Passed 1.75 sec -67: ..... -67: ---------------------------------------------------------------------- -67: Ran 19 tests in 2.081s -67: -67: OK -141: [03:35:39] ------------------------------------- -141: [03:35:39] Test MMFF atom types. -141: [03:35:39] done -141: [03:35:39] ------------------------------------- -141: [03:35:39] Testing MMFF builder tools. -142: [03:35:39] ------------------------------------- -142: [03:35:39] Test MMFF multithreading -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: [13:04:23] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] ------------------------------------- +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: ........[13:04:23] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +97: [13:04:23] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +97: [13:04:23] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +97: [13:04:23] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +97: .[13:04:23] reactant atom-mapping number 1 found multiple times. +97: [13:04:23] product atom-mapping number 2 not found in reactants. +97: [13:04:23] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 4 +97: [13:04:23] product atom-mapping number 5 not found in reactants. +147: Randomness seeded to: 518640331 +128: [13:04:23] ------------------------------------- +146: [13:04:22] ******************************************************** +146: [13:04:22] Testing DistGeomHelpers +146: [13:04:22] --------------------------------- +146: [13:04:22] test2 +146: +146: go +146: ------------------------------------- +146: +128: [13:04:23] ------------------------------------- +128: [13:04:23] ------------------------------------- +128: [13:04:23] Test Atom Pairs including info about chirality. +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] done +128: [13:04:23] ------------------------------------- +128: [13:04:23] Test Topological Torsions including info about chirality. +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] done +128: [13:04:23] ------------------------------------- +128: [13:04:23] Test GitHub Issue 25: fingerprint backwards compatibility. +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] done +128: [13:04:23] ------------------------------------- +128: [13:04:23] Test GitHub Issue 151: PatternFingerprint problems +67: ..............[13:04:23] SMILES Parse Error: syntax error while parsing: invalidsmiles +67: [13:04:23] SMILES Parse Error: check for mistakes around position 1: +67: [13:04:23] invalidsmiles +67: [13:04:23] ^ +67: [13:04:23] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: [13:04:23] done +128: [13:04:23] ------------------------------------- +128: [13:04:23] Test 3D atom pairs. +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:23] done +128: [13:04:23] ------------------------------------- +128: [13:04:23] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +128: [13:04:23] done +128: [13:04:23] ------------------------------------- +128: [13:04:23] Test multithreading with the pattern FP +128: reading molecules +106/238 Test #110: pyFragCatalog .......................... Passed 3.76 sec test 148 Start 148: pyDistGeomHelpers 148: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 148: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 148: Test timeout computed to be: 1500 +142: processing +142: launch :0 +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +142: launch :1 +142: launch :2 +142: launch :3 +142: launch :4 +142: launch :5 +142: launch :6 +142: launch :7 +142: launch :8 +142: launch :9 +142: launch :10 +142: launch :11 +142: launch :12 +142: launch :13 +142: launch :14 +142: launch :15 +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [13:04:23] done +141: [13:04:23] ------------------------------------- +141: [13:04:23] Testing Issue239. +142: launch :16 +142: launch :17 +142: launch :18 +142: launch :19 +142: launch :20 +142: launch :21 +142: launch :22 +142: launch :23 +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +89: [13:04:23] Explicit valence for atom # 2 O, 4, is greater than permitted +147: [13:04:23] [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: [13:04:23] [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)] +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: pass 1 128: launch :0 +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 128: launch :1 128: launch :2 128: launch :3 -140: Randomness seeded to: 2830189252 -140: =============================================================================== -140: All tests passed (17 assertions in 2 test cases) -140: -143: [03:35:39] ------------------------------------- -143: [03:35:39] Test UFF atom labels. -143: [03:35:39] done -143: [03:35:39] ------------------------------------- -143: [03:35:39] Test UFF atom typer. -143: [03:35:39] done -143: [03:35:39] ------------------------------------- -143: [03:35:39] Testing UFF builder tools. -143: [03:35:39] done -143: [03:35:39] ------------------------------------- -143: [03:35:39] Testing UFF builder+minimization. -144: ------------------------------------- -144: Test CrystalFF torsional term. -109/238 Test #110: pyFragCatalog .......................... Passed 2.23 sec -110/238 Test #140: forceFieldHelpersCatch ................. Passed 0.06 sec -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -test 149 - Start 149: testMolAlign - -149: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign -149: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign -149: Test timeout computed to be: 1500 -test 150 - Start 150: testO3AAlign - -150: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign -150: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign -150: Test timeout computed to be: 1500 -141: [03:35:39] done -141: [03:35:39] ------------------------------------- -141: [03:35:39] Testing MMFF builder+minimization. -68: Test -68: -68: AlexRxn.mrv -68: -68: Test -68: -68: BadReactionSign.mrv -68: +89: [13:04:23] Explicit valence for atom # 3 Be, 4, is greater than permitted +89: [13:04:23] Explicit valence for atom # 3 Al, 6, is greater than permitted +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [13:04:23] [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: [13:04:23] [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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [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: [13:04:23] [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: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [13:04:23] [*: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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [$([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)] +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [13:04:23] [$(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: [13:04:23] [$(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: [13:04:23] [$(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: [13:04:23] [$(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: [13:04:23] [$(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: [13:04:23] [$(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: [13:04:23] [$(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: [13:04:23] [$(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)] +97: ........./build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> +97: png = open(fname, 'rb').read() +97: ResourceWarning: Enable tracemalloc to get the object allocation traceback +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [13:04:23] [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: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] 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)] +141: [13:04:23] done +141: [13:04:23] ------------------------------------- +141: [13:04:23] Testing calcEnergy with passed coords. +89: [13:04:23] Explicit valence for atom # 27 P, 6, is greater than permitted +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [13:04:23] [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: [13:04:23] [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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [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)] +97: [13:04:23] Found a SCD/SED line with missing/empty SDT specification at line 34 +97: [13:04:23] Found a SCD/SED line with missing/empty SDT specification at line 36 +97: [13:04:23] Found a SCD/SED line with missing/empty SDT specification at line 38 +97: [13:04:23] Found a SCD/SED line with missing/empty SDT specification at line 40 +97: [13:04:23] Found a SCD/SED line with missing/empty SDT specification at line 42 +147: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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)] +97: [13:04:23] Found a SCD/SED line with missing/empty SDT specification at line 87 +97: [13:04:23] Found a SCD/SED line with missing/empty SDT specification at line 89 +97: [13:04:23] Found a SCD/SED line with missing/empty SDT specification at line 91 +97: [13:04:23] Found a SCD/SED line with missing/empty SDT specification at line 93 +97: [13:04:23] Found a SCD/SED line with missing/empty SDT specification at line 95 +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: ----------- +147: [13:04:23] [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: [13:04:23] [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: [13:04:23] [$([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: [13:04:23] [$([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: [13:04:23] [$(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: [13:04:23] [$(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: [13:04:23] [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: [13:04:23] [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)] +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [13:04:23] 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: [13:04:23] 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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [!#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: [13:04:23] [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: [13:04:23] [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)] +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: ----------- +147: [13:04:23] [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)] +143: [13:04:23] done +143: [13:04:23] ------------------------------------- +143: [13:04:23] Testing UFF special cases. +143: [13:04:23] UFFTYPER: Unrecognized charge state for atom: 0 +143: [13:04:23] done +143: [13:04:23] ------------------------------------- +143: [13:04:23] Testing Issue239. +147: [13:04:23] [$([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: [13:04:23] [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: [13:04:23] 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: ----------- +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: ..[13:04:23] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [13:04:23] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +141: [13:04:23] done +141: [13:04:23] ------------------------------------- +141: [13:04:23] Testing calcGrad. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: ----------- +147: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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)] 68: Test 68: -68: bondArray_node.mrv +68: FalseAtropisomer.mrv 68: 68: Test 68: -68: marvin03.mrv +68: AtropEnhancedStereo.mrv 68: 68: Test 68: -68: marvin04.mrv +68: AtropManyChirals.mrv 68: 68: Test 68: -68: marvin08.mrv +68: AtropManyChiralsEnhanced.mrv 68: 68: Test 68: -68: marvin09.mrv +68: AtropManyChiralsEnhanced2.mrv 68: 68: Test 68: -68: marvin11.mrv +68: AtropManyChiralsEnhanced3.mrv 68: 68: Test 68: -68: marvin05.mrv +68: AtropManyChiralsEnhanced4.mrv 68: 68: Test 68: -68: EmptyRxn.mrv +68: BMS-986142_3d_chiral.mrv 68: -68: [03:35:39] initialization failed -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 400 -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -146: [03:35:39] ******************************************************** -146: [03:35:39] Testing DistGeomHelpers -146: [03:35:39] --------------------------------- -146: [03:35:39] test2 -146: -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -146: go -146: ------------------------------------- -146: -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -142: processing -142: launch :0 -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -142: launch :1 -142: launch :2 -142: launch :3 -142: launch :4 -142: launch :5 -142: launch :6 -142: launch :7 -142: launch :8 -142: launch :9 -142: launch :10 -142: launch :11 -142: launch :12 -142: launch :13 -142: launch :14 -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -142: launch :15 -142: launch :16 -142: launch :17 -142: launch :18 -142: launch :19 -142: launch :20 -142: launch :21 -142: launch :22 -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -142: launch :23 -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: Randomness seeded to: 1774957625 -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: RxnNoCoords.mrv +68: BMS-986142_3d.mrv 68: 68: Test 68: -68: mrvValenceZero.mrv +68: BMS-986142_atrop1.mrv 68: 68: Test 68: -68: condition_coordinates_mpoint.mrv +68: BMS-986142_atrop2.mrv 68: 68: Test 68: -68: marvin01.mrv +68: BMS-986142_atrop3.mrv 68: 68: Test 68: -68: aspirineSynthesisWithAttributes.mrv +68: BMS-986142_atrop4.mrv 68: 68: Test 68: -68: marvin01.mrv +68: BMS-986142_atrop5.mrv 68: +97: [13:04:23] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [13:04:23] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +68: [13:04:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [13:04:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +143: [13:04:23] done +147: [13:04:23] [$(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: [13:04:23] [$(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: [13:04:23] [$(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)] +143: [13:04:23] ------------------------------------- +143: [13:04:23] Testing calcEnergy with passed coords. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: [13:04:23] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [13:04:23] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [13:04:23] reaction has no reactants +97: [13:04:23] reaction has no products +97: [13:04:23] initialization failed +97: [13:04:23] reaction has no reactants +97: [13:04:23] reaction has no products +147: [13:04:23] [$(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: [13:04:23] [$(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: [13:04:23] [$(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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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: [13:04:23] [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)] +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [13:04:23] done +143: [13:04:23] ------------------------------------- +143: [13:04:23] Testing calcGrad. +97: .[13:04:23] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [13:04:23] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +107/238 Test #144: testCrystalForceField .................. Passed 0.53 sec +test 149 + Start 149: testMolAlign + +149: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign +149: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign +149: Test timeout computed to be: 1500 +97: [13:04:23] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [13:04:23] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [13:04:23] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [13:04:23] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: [13:04:23] reaction has no reactants +97: [13:04:23] reaction has no products +97: [13:04:23] initialization failed +97: [13:04:23] reaction has no reactants +97: [13:04:23] reaction has no products +97: . +97: ---------------------------------------------------------------------- +97: Ran 54 tests in 0.723s +97: +97: OK +97: ******************************************** +97: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +97: +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: NewChiralTest +68: BMS-986142_atrop6.mrv 68: 68: Test 68: -68: NewChiralTest +68: BMS-986142_atrop7.mrv 68: 68: Test 68: -68: NewChiralTestNoChiral +68: BMS-986142_atrop8.mrv 68: +68: [13:04:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [13:04:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +143: [13:04:23] done +143: [13:04:23] ------------------------------------- +143: [13:04:23] Testing SFIssue1653802. +143: [13:04:23] done +143: [13:04:23] ------------------------------------- +143: [13:04:23] Testing SFIssue2378119. +141: [13:04:23] done +141: [13:04:23] ------------------------------------- +141: [13:04:23] Testing Issue242. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [13:04:23] done +143: [13:04:23] ------------------------------------- +143: [13:04:23] Test UFF force-field parameter getters. +143: [13:04:23] ------------------------------------- +143: [13:04:23] Testing handling missing parameters. +143: [13:04:23] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [13:04:23] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: [13:04:23] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [13:04:23] UFFTYPER: Unrecognized atom type: Cu+1 (0) +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: NewChiralTestNoChiral +68: BMS-986142_atropBad2.mrv 68: +68: [13:04:23] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +35: [13:04:23] Maximum BFS search size exceeded. +35: This is likely due to a highly symmetric fused ring system. +143: [13:04:23] done +143: [13:04:23] ------------------------------------- +143: [13:04:23] Testing SFIssue3009337. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143: [13:04:23] done +143: [13:04:23] ------------------------------------- +143: [13:04:23] Test UFF multithreading +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +142: done +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: [13:04:23] done +141: [13:04:23] ------------------------------------- +141: [13:04:23] Testing github 308: crash during MMFF parameterization . +141: [13:04:23] ------------------------------------- +141: [13:04:23] Testing SFIssue1653802. +141: [13:04:23] done +141: [13:04:23] ------------------------------------- +141: [13:04:23] Testing SFIssue2378119. +141: [13:04:23] done +141: [13:04:23] ------------------------------------- +141: [13:04:23] Test MMFF force-field parameter getters. +141: [13:04:23] ------------------------------------- +141: [13:04:23] Test MMFF multithreading +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] 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: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +141: generating reference data +142: [13:04:23] done 68: Test 68: -68: NewChiralTest2 +68: JDQ443_3d.mrv 68: 68: Test 68: -68: NewChiralTest2 +68: JDQ443_atrop1.mrv 68: 68: Test 68: -68: NewChiralTest2AllChiral +68: JDQ443_atrop2.mrv 68: 68: Test 68: -68: NewChiralTest2AllChiral +68: JDQ443_atrop3.mrv 68: 68: Test 68: -68: Vendor839 +68: JDQ443_atropBad1.mrv 68: +68: [13:04:23] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 400 +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [13:04:23] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +35: F/C=C/Cl +35: [H]/C(F)=C(/[H])Cl +35: F/C=C/Cl +35: F/C=C/Cl +35: C/C(F)=C(/C)Cl +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: DoubleBondChain +68: RP-6306_atrop1.mrv 68: 68: Test 68: -68: Na_Mg_Al_OH +68: RP-6306_atrop2.mrv 68: 68: Test 68: -68: Pb +68: RP-6306_atrop3.mrv 68: 68: Test 68: -68: O_Mg_Si +68: RP-6306_atrop4.mrv 68: 68: Test 68: -68: SquiggleBond +68: RP-6306_atrop5.mrv 68: +68: [13:04:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [13:04:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 68: Test 68: -68: BigMacrocycle +68: RP-6306_atropBad1.mrv 68: +68: [13:04:23] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [13:04:23] UFFTYPER: Unrecognized charge state for atom: 1 +128: pass 2 +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +67: ..... +67: ---------------------------------------------------------------------- +67: Ran 19 tests in 3.962s +67: +67: OK +35: [13:04:23] ----------------------- +35: Testing isRingFused 68: Test 68: -68: Smiles1 +68: RP-6306_atropBad2.mrv 68: -111/238 Test #68: testMrvToMol ........................... Passed 2.49 sec +68: [13:04:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [13:04:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +68: [13:04:23] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108/238 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.85 sec +test 150 + Start 150: testO3AAlign + +150: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign +150: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign +150: Test timeout computed to be: 1500 +147: [13:04:23] UFFTYPER: Unrecognized charge state for atom: 1 +125: Warning: Atom Count for residue ASN39A does not match expected count +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +109/238 Test #97: pyChemReactions ........................ Passed 4.60 sec test 151 Start 151: molAlignCatchTest 151: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 151: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 151: Test timeout computed to be: 1500 -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:39] Explicit valence for atom # 3 Al, 6, is greater than permitted -112/238 Test #67: pyDepictor ............................. Passed 2.50 sec -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +110/238 Test #35: graphmolMolOpsTest ..................... Passed 5.42 sec test 152 Start 152: pyMolAlign 152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 152: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap 152: Test timeout computed to be: 1500 -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [03:35:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:35:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:35:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:35:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [03:35:39] deprecated group abbreviation ignored on line 24 -69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [03:35:39] -69: -69: **** -69: Post-condition Violation -69: Element 'Mv' not found -69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -69: Failed Expression: anum > -1 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 3# 0x00007FD141CC8511 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x00007FD141CD1DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x00007FD141CD214D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 9# 0x0000563E0ECC3C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x0000563E0ED2A3F2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x0000563E0ECAA923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x00007FD141233CA8 in /lib/x86_64-linux-gnu/libc.so.6 -69: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -69: 14# 0x0000563E0ECAAAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [03:35:39] done -143: [03:35:39] ------------------------------------- -143: [03:35:39] Testing UFF special cases. -143: [03:35:39] UFFTYPER: Unrecognized charge state for atom: 0 -143: [03:35:39] done -143: [03:35:39] ------------------------------------- -143: [03:35:39] Testing Issue239. -147: [03:35:39] [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)] -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [03:35:39] [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)] -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [03:35:39] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [03:35:39] [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: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [03:35:39] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [03:35:39] [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)] -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [03:35:39] [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: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [03:35:39] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -143: [03:35:39] done -143: [03:35:39] ------------------------------------- -143: [03:35:39] Testing calcEnergy with passed coords. -147: [03:35:39] [$([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)] -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [03:35:39] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$(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)] -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [03:35:39] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [03:35:39] [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)] -141: [03:35:39] done -141: [03:35:39] ------------------------------------- -141: [03:35:39] Testing Issue239. -113/238 Test #144: testCrystalForceField .................. Passed 0.15 sec -test 153 - Start 153: testFeatures - -153: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures -153: Test timeout computed to be: 1500 -147: [03:35:39] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [03:35:39] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [03:35:39] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: ----------- -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [03:35:39] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [03:35:39] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$(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: [03:35:39] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [03:35:39] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] -147: [03:35:39] [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: ----------- -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:39] Explicit valence for atom # 4 Al, 6, is greater than permitted -143: [03:35:39] done -143: [03:35:39] ------------------------------------- -143: [03:35:39] Testing calcGrad. -143: [03:35:39] done -143: [03:35:39] ------------------------------------- -143: [03:35:39] Testing SFIssue1653802. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [13:04:23] UFFTYPER: Unrecognized charge state for atom: 1 +127: ........ +127: ---------------------------------------------------------------------- +127: Ran 8 tests in 0.183s +127: +127: OK +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 149: *********************************************************** 149: Testing MolAlign 149: --------------------------------- @@ -25760,139 +25589,180 @@ 149: testIssue241 149: 149: *********************************************************** -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [03:35:39] [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)] -114/238 Test #149: testMolAlign ........................... Passed 0.13 sec -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111/238 Test #127: pyMolDescriptors3D ..................... Passed 1.57 sec +test 153 + Start 153: testFeatures + +153: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures +153: Test timeout computed to be: 1500 +112/238 Test #149: testMolAlign ........................... Passed 0.42 sec test 154 Start 154: pyChemicalFeatures 154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 154: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 154: Test timeout computed to be: 1500 -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [03:35:39] done -143: [03:35:39] ------------------------------------- -143: [03:35:39] Testing SFIssue2378119. -143: [03:35:39] done -143: [03:35:39] ------------------------------------- -143: [03:35:39] Test UFF force-field parameter getters. -143: [03:35:39] ------------------------------------- -143: [03:35:39] Testing handling missing parameters. -143: [03:35:39] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [03:35:39] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: [03:35:39] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [03:35:39] UFFTYPER: Unrecognized atom type: Cu+1 (0) -147: [03:35:39] 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: [03:35:39] done -130: [03:35:39] ------------------------------------- -130: [03:35:39] Test unfolded version of RDKFP -130: [03:35:39] ------------------------------------- -130: [03:35:39] Test topological torsion fp generator -130: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -153: [03:35:39] ------------------------------------- -153: [03:35:39] AtomType parser testing. -153: [03:35:39] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -153: [03:35:39] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -153: [03:35:39] done -153: [03:35:39] ------------------------------------- -153: [03:35:39] FeatureDefinition parser testing. -153: [03:35:39] done -153: [03:35:39] ------------------------------------- -153: [03:35:39] Test pulling feat defs from a string. -153: [03:35:39] done -153: [03:35:39] ------------------------------------- -153: [03:35:39] FeatureDef functionality testing. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [03:35:39] done -141: [03:35:39] ------------------------------------- -141: [03:35:39] Testing calcEnergy with passed coords. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: ----------- -143: [03:35:39] done -143: [03:35:39] ------------------------------------- -143: [03:35:39] Testing SFIssue3009337. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -143: [03:35:39] done -143: [03:35:39] ------------------------------------- -143: [03:35:39] Test UFF multithreading -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [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)] -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [03:35:39] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [03:35:39] [$(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)] -130: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [03:35:39] Explicit valence for atom # 10 Si, 6, is greater than permitted -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -147: [03:35:39] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [03:35:39] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [03:35:39] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [03:35:39] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [03:35:39] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [03:35:39] [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: [03:35:39] done -153: [03:35:39] ------------------------------------- -153: [03:35:39] FeatureFactory testing. -153: [03:35:39] 1 -153: [03:35:39] 2 -153: [03:35:39] 3 -153: [03:35:39] 4 -153: [03:35:39] 5 -153: [03:35:39] 6 -153: [03:35:39] done -153: [03:35:39] ------------------------------------- -153: [03:35:39] Feature Location testing. -153: [03:35:39] done -153: [03:35:39] ------------------------------------- -153: [03:35:39] Test building a FeatureFactory from a file -153: [03:35:39] done -153: [03:35:39] ------------------------------------- -153: [03:35:39] Testing Issue 224. -153: [03:35:39] done -153: [03:35:39] ------------------------------------- -153: [03:35:39] Testing Issue 225. -153: [03:35:39] done -153: [03:35:39] ------------------------------------- -153: [03:35:39] Test Issue346 -153: [03:35:39] done -153: [03:35:39] ------------------------------------- -153: [03:35:39] Test Issue347 -153: [03:35:39] done -153: [03:35:39] ------------------------------------- -153: [03:35:39] Testing Issue 348. -153: [03:35:39] SMARTS Parse Error: syntax error while parsing: [C[C] -153: [03:35:39] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -153: [03:35:39] ------------------------------------- -153: [03:35:39] Testing Nested AtomType definitions. +68: Test +68: +68: RP-6306_3d.mrv +68: +68: Test +68: +68: Sotorasib_atrop1.mrv +68: +68: Test +68: +68: Sotorasib_atrop2.mrv +68: +68: Test +68: +68: Sotorasib_atrop3.mrv +68: +68: Test +68: +68: Sotorasib_atrop4.mrv +68: +68: Test +68: +68: Sotorasib_atrop5.mrv +68: +68: [13:04:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +68: [13:04:23] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +134: .. +134: ---------------------------------------------------------------------- +134: Ran 2 tests in 0.144s +134: +134: OK +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: Sotorasib_atropBad1.mrv +68: +68: [13:04:23] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +153: [13:04:23] ------------------------------------- +153: [13:04:23] AtomType parser testing. +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: .[13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:23] DEPRECATION WARNING: please use AtomPairGenerator +153: [13:04:23] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +153: [13:04:23] 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: [13:04:23] done +153: [13:04:23] ------------------------------------- +153: [13:04:23] FeatureDefinition parser testing. +145: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +153: [13:04:23] done +153: [13:04:23] ------------------------------------- +153: [13:04:23] Test pulling feat defs from a string. +153: [13:04:23] done +153: [13:04:23] ------------------------------------- +153: [13:04:23] FeatureDef functionality testing. +145: [13:04:23] Molecule does not have explicit Hs. Consider calling AddHs() +145: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [13:04:23] Molecule does not have explicit Hs. Consider calling AddHs() +145: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [13:04:23] Molecule does not have explicit Hs. Consider calling AddHs() +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] 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: [13:04:23] test on : 365 molecules done +145: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [13:04:23] Molecule does not have explicit Hs. Consider calling AddHs() +145: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: Sotorasib_atropBad2.mrv +68: +68: [13:04:23] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +136: ....... +136: ---------------------------------------------------------------------- +136: Ran 7 tests in 0.279s +136: +136: OK +145: [13:04:23] Molecule does not have explicit Hs. Consider calling AddHs() +145: ..[13:04:23] Molecule does not have explicit Hs. Consider calling AddHs() +145: [13:04:23] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[13:04:23] 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 0.342s +133: +133: OK +153: [13:04:23] done +153: [13:04:23] ------------------------------------- +153: [13:04:23] FeatureFactory testing. +153: [13:04:23] 1 +153: [13:04:23] 2 +153: [13:04:23] 3 +153: [13:04:23] 4 +153: [13:04:23] 5 +153: [13:04:23] 6 +153: [13:04:23] done +153: [13:04:23] ------------------------------------- +153: [13:04:23] Feature Location testing. +153: [13:04:23] done +153: [13:04:23] ------------------------------------- +153: [13:04:23] Test building a FeatureFactory from a file +145: [13:04:23] Molecule does not have explicit Hs. Consider calling AddHs() +153: [13:04:23] done +153: [13:04:23] ------------------------------------- +153: [13:04:23] Testing Issue 224. +153: [13:04:23] done +153: [13:04:23] ------------------------------------- +153: [13:04:23] Testing Issue 225. +153: [13:04:23] done +153: [13:04:23] ------------------------------------- +153: [13:04:23] Test Issue346 +153: [13:04:23] done +153: [13:04:23] ------------------------------------- +153: [13:04:23] Test Issue347 +153: [13:04:23] done +153: [13:04:23] ------------------------------------- +153: [13:04:23] Testing Issue 348. +153: [13:04:23] SMARTS Parse Error: syntax error while parsing: [C[C] +153: [13:04:23] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +153: [13:04:23] ------------------------------------- +153: [13:04:23] Testing Nested AtomType definitions. 153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -153: [03:35:39] ------------------------------------- -153: [03:35:39] Testing Github Issue #252: crash when calling getPos() with no conformer. -153: [03:35:39] expect a precondition failure message below -153: [03:35:39] +153: [13:04:23] ------------------------------------- +153: [13:04:23] Testing Github Issue #252: crash when calling getPos() with no conformer. +153: [13:04:23] expect a precondition failure message below +153: [13:04:23] 153: 153: **** 153: Pre-condition Violation @@ -25905,98 +25775,31 @@ 153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -153: 4# 0x000055F059D91E50 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 5# 0x000055F059D86743 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 6# 0x00007F5840233CA8 in /lib/x86_64-linux-gnu/libc.so.6 +153: 4# 0x000055779F55DE50 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 5# 0x000055779F552743 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 6# 0x00007FB56A033CA8 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# 0x000055F059D86841 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 8# 0x000055779F552841 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: ---------- 153: **** 153: -153: [03:35:39] Done -153: [03:35:39] ------------------------------------- -153: [03:35:39] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -153: [03:35:39] done -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115/238 Test #153: testFeatures ........................... Passed 0.03 sec +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +126: ..[13:04:23] +126: +126: **** +153: [13:04:23] Done +153: [13:04:23] ------------------------------------- +153: [13:04:23] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +153: [13:04:23] done +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +113/238 Test #118: testRDF ................................ Passed 4.29 sec test 155 Start 155: testShapeHelpers 155: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 155: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers 155: Test timeout computed to be: 1500 -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: Elapsed time: 2.31483 s -115: Errors:0 -115: [03:35:39] test on : 500 molecules done -141: [03:35:39] done -141: [03:35:39] ------------------------------------- -141: [03:35:39] Testing calcGrad. -130: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [03:35:39] done -130: [03:35:39] ------------------------------------- -130: [03:35:39] Test Topological Torsions. -130: [03:35:39] done -130: [03:35:39] ------------------------------------- -130: [03:35:39] Test Folded torsions. -130: [03:35:39] done -130: [03:35:39] ------------------------------------- -130: [03:35:39] Test Bulk Topological Torsions. -143: generating reference data -116/238 Test #115: testEEM ................................ Passed 2.35 sec -test 156 - Start 156: pyShapeHelpers - -156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" -156: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap -156: Test timeout computed to be: 1500 -141: [03:35:39] done -141: [03:35:39] ------------------------------------- -141: [03:35:39] Testing Issue242. -151: Randomness seeded to: 1123282151 -151: 64730073 -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:39] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: .[03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:39] DEPRECATION WARNING: please use AtomPairGenerator -126: ..[03:35:39] -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 @@ -26006,10 +25809,10 @@ 126: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 126: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/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-202503.1/obj-x86_64-linux-gnu//lib/libRDKitDescriptors.so.1 -126: 3# 0x00007FC16D36C43A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -126: 4# 0x00007FC16D37C726 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 3# 0x00007F06E6E9743A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 4# 0x00007F06E6EA7726 in /build/reproducible-path/rdkit-202503.1/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# 0x00007FC17140662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +126: 6# 0x00007F06EAF4062C 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-202503.1/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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -26020,17 +25823,17 @@ 126: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-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-202503.1/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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 17# 0x00007FC16EFB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 18# 0x00007FC16EFB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 19# 0x00007FC16EFB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 20# 0x00007FC16EFB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -126: 21# 0x00007FC16EFB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 17# 0x00007F06E8BB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 18# 0x00007F06E8BB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 19# 0x00007F06E8BB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 20# 0x00007F06E8BB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +126: 21# 0x00007F06E8BB7933 in /build/reproducible-path/rdkit-202503.1/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-202503.1/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-202503.1/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-202503.1/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-202503.1/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# 0x00007FC1714033C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +126: 27# 0x00007F06EAF3D3C6 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# 0x00000000005CBA19 in /usr/bin/python3 @@ -26062,396 +25865,292 @@ 126: 56# 0x00000000006B339E in /usr/bin/python3 126: 57# Py_RunMain in /usr/bin/python3 126: 58# Py_BytesMain in /usr/bin/python3 -126: 59# 0x00007FC171CD2CA8 in /lib/x86_64-linux-gnu/libc.so.6 +126: 59# 0x00007F06EB80CCA8 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: -141: [03:35:39] done -141: [03:35:39] ------------------------------------- -141: [03:35:39] Testing github 308: crash during MMFF parameterization . -141: [03:35:39] ------------------------------------- -141: [03:35:39] Testing SFIssue1653802. -155: *********************************************************** -155: Testing ShapeHelpers -155: --------------------------------- -155: test1Encode -155: -155: --------------------------------- -155: test2Compare -155: -155: --------------------------------- -155: testGithub4364 -155: -155: *********************************************************** -117/238 Test #155: testShapeHelpers ....................... Passed 0.05 sec +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +139: ........ +139: ---------------------------------------------------------------------- +139: Ran 8 tests in 0.125s +139: +139: OK +114/238 Test #153: testFeatures ........................... Passed 0.07 sec +test 156 + Start 156: pyShapeHelpers + +156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" +156: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap +156: Test timeout computed to be: 1500 +145: .[13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [13:04:23] Molecule does not have explicit Hs. Consider calling AddHs() +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +120: [13:04:23] done +120: [13:04:23] ------------------------------------- +120: [13:04:23] PMI edge cases. +120: [13:04:23] done +120: [13:04:23] ------------------------------------- +120: [13:04:23] NPR edge cases. +120: [13:04:23] done +120: [13:04:23] ------------------------------------- +120: [13:04:23] 3D descriptors. +120: [13:04:23] done +120: [13:04:23] ------------------------------------- +120: [13:04:23] 3D descriptor edge cases. +120: [13:04:23] done +120: [13:04:23] ------------------------------------- +120: [13:04:23] Inertial shape factor. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +120: [13:04:23] done +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115/238 Test #67: pyDepictor ............................. Passed 5.18 sec test 157 Start 157: testMolCatalog 157: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 157: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog 157: Test timeout computed to be: 1500 -141: [03:35:39] done -141: [03:35:39] ------------------------------------- -141: [03:35:39] Testing SFIssue2378119. -141: [03:35:39] done -141: [03:35:39] ------------------------------------- -141: [03:35:39] Test MMFF force-field parameter getters. -141: [03:35:39] ------------------------------------- -141: [03:35:39] Test MMFF multithreading -117: =>start test morse custom -117: [03:35:39] test on : 365 molecules done -151: 34424151 -147: [03:35:39] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -141: generating reference data -139: ........ -139: ---------------------------------------------------------------------- -139: Ran 8 tests in 0.033s -139: -139: OK -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 -147: [03:35:39] UFFTYPER: Unrecognized charge state for atom: 1 -126: Warning: Atom Count for residue ARG64A does not match expected count -126: Warning: Atom Count for residue LYS80A does not match expected count -147: [03:35:39] UFFTYPER: Unrecognized charge state for atom: 1 -127: ........ -127: ---------------------------------------------------------------------- -127: Ran 8 tests in 0.200s -127: -127: OK -118/238 Test #157: testMolCatalog ......................... Passed 0.04 sec +116/238 Test #120: test3D ................................. Passed 4.16 sec test 158 Start 158: pyMolCatalog 158: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 158: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 158: Test timeout computed to be: 1500 -128: pass 2 -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -126: Warning: Atom Count for residue GLU150A does not match expected count -126: Warning: Atom Count for residue ASN157A does not match expected count -147: [03:35:39] UFFTYPER: Unrecognized charge state for atom: 1 -69: [03:35:39] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -69: [03:35:39] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -119/238 Test #139: pyMolTransforms ........................ Passed 0.33 sec +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] 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 GLU5A does not match expected count +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +130: [13:04:23] done +130: [13:04:23] ------------------------------------- +130: [13:04:23] Test unfolded version of RDKFP +130: [13:04:23] ------------------------------------- +130: [13:04:23] Test topological torsion fp generator +130: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +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 +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] 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: [13:04:23] test on : 365 molecules done +126: Warning: Atom Count for residue LYS80A does not match expected count +117/238 Test #119: testMORSE .............................. Passed 4.39 sec +118/238 Test #136: pyPartialCharges ....................... Passed 1.20 sec +130: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator test 159 Start 159: moldraw2DTest1 159: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 159: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 159: Test timeout computed to be: 1500 -134: .. -134: ---------------------------------------------------------------------- -134: Ran 2 tests in 0.079s -134: -134: OK -136: ....... -136: ---------------------------------------------------------------------- -136: Ran 7 tests in 0.126s -136: -136: OK -120/238 Test #127: pyMolDescriptors3D ..................... Passed 2.18 sec test 160 Start 160: moldraw2DTestCatch 160: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 160: Test timeout computed to be: 1500 -130: [03:35:39] done -130: [03:35:39] ------------------------------------- -130: [03:35:39] Test Rooted Topological Torsions. -130: [03:35:39] done -130: [03:35:39] ------------------------------------- -130: [03:35:39] Test ignoring atoms in Topological Torsions. -130: [03:35:39] done -130: [03:35:39] ------------------------------------- -130: [03:35:39] ------------------------------------- -130: [03:35:39] Test Topological Torsions including info about chirality. -130: [03:35:39] done -130: [03:35:39] ------------------------------------- -130: [03:35:39] Test GitHub Issue 25: fingerprint backwards compatibility. -130: [03:35:39] done -130: [03:35:39] ------------------------------------- -130: [03:35:39] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -159: ----------------- Test 1 -130: [03:35:39] done -130: [03:35:39] ------------------------------------- -130: [03:35:39] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -35: [03:35:39] Maximum BFS search size exceeded. -35: This is likely due to a highly symmetric fused ring system. -130: [03:35:39] done -130: [03:35:39] ------------------------------------- -130: [03:35:39] Test convenience and bulk fp calculation functions -125: Warning: Atom Count for residue ASN39A does not match expected count -145: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -142: done -145: [03:35:39] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:39] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:39] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:39] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:39] Molecule does not have explicit Hs. Consider calling AddHs() -145: ..[03:35:39] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:35:39] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:39] Molecule does not have explicit Hs. Consider calling AddHs() -121/238 Test #136: pyPartialCharges ....................... Passed 2.03 sec -126: Warning: Atom Count for residue GLU5A does not match expected count +130: [13:04:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +89: [13:04:23] Explicit valence for atom # 9 N, 5, is greater than permitted +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +68: Test +68: +68: Sotorasib_3d.mrv +68: +68: Test +68: +68: ZM374979_atrop1.mrv +68: +68: Test +68: +68: ZM374979_atrop2.mrv +68: +68: Test +68: +68: ZM374979_atrop3.mrv +68: +68: Test +68: +68: ZM374979_atropBad1.mrv +68: +68: [13:04:23] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +155: *********************************************************** +155: Testing ShapeHelpers +155: --------------------------------- +155: test1Encode +155: +155: --------------------------------- +155: test2Compare +155: +155: --------------------------------- +155: testGithub4364 +155: +155: *********************************************************** +119/238 Test #155: testShapeHelpers ....................... Passed 0.14 sec +145: .[13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [13:04:23] Molecule does not have explicit Hs. Consider calling AddHs() test 161 Start 161: moldraw2DRxnTest1 161: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 161: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 161: Test timeout computed to be: 1500 -89: [03:35:39] Explicit valence for atom # 2 O, 4, is greater than permitted -145: .[03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:39] Molecule does not have explicit Hs. Consider calling AddHs() -159: file test1_5.svg gave hash 2383324771U not the expected 2811480876U -159: Done -159: ----------------- Test 2 -69: ---------------------------------- -142: [03:35:39] done -69: ---------------------------------- -122/238 Test #134: pyTestMHFP ............................. Passed 2.06 sec -89: [03:35:39] Explicit valence for atom # 3 Be, 4, is greater than permitted +115: [13:04:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:23] 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 +126: Warning: Atom Count for residue ASN157A does not match expected count +151: Randomness seeded to: 1559475561 +151: 146047306 +120/238 Test #134: pyTestMHFP ............................. Passed 1.41 sec test 162 Start 162: pyMolDraw2D 162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" 162: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap 162: Test timeout computed to be: 1500 -89: [03:35:39] Explicit valence for atom # 3 Al, 6, is greater than permitted -69: [03:35:39] -69: -69: **** -69: Pre-condition Violation -69: rlabel out of range for MDL files -69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp -69: Failed Expression: rlabel >= 0 && rlabel < 100 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -69: 3# 0x0000563E0ECD0FFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x0000563E0ED2A46A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x0000563E0ECAA923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x00007FD141233CA8 in /lib/x86_64-linux-gnu/libc.so.6 -69: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -69: 8# 0x0000563E0ECAAAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -69: [03:35:39] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -159: file test2_1.png gave hash 240594419U not the expected 638584804U -159: file test2_2.png gave hash 278647755U not the expected 610424244U -145: .[03:35:39] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:39] Molecule does not have explicit Hs. Consider calling AddHs() -161: ----------------- Test 1 -35: F/C=C/Cl -35: [H]/C(F)=C(/[H])Cl -35: F/C=C/Cl -35: F/C=C/Cl -35: C/C(F)=C(/C)Cl -159: Done -159: ----------------- Test 4 -89: [03:35:40] Explicit valence for atom # 27 P, 6, is greater than permitted -160: Randomness seeded to: 2133221184 -160: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U -145: .[03:35:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -159: file test4_1.png gave hash 509333604U not the expected 3993974247U -159: Done -159: ----------------- Test 5 -123/238 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.45 sec +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +130: [13:04:24] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [13:04:24] done +130: [13:04:24] ------------------------------------- +130: [13:04:24] Test Topological Torsions. +130: [13:04:24] done +130: [13:04:24] ------------------------------------- +130: [13:04:24] Test Folded torsions. +130: [13:04:24] done +130: [13:04:24] ------------------------------------- +130: [13:04:24] Test Bulk Topological Torsions. +145: .[13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +121/238 Test #157: testMolCatalog ......................... Passed 0.11 sec test 163 Start 163: testFMCS 163: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/testFMCS 163: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS 163: Test timeout computed to be: 1500 -159: file test5_1.png gave hash 650561118U not the expected 571291290U -161: file rxn_test1_1.png gave hash 760679292U not the expected 801892091U -145: .[03:35:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -147: [03:35:40] UFFTYPER: Unrecognized charge state for atom: 5 -145: .[03:35:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[03:35:40] UFFTYPER: Unrecognized hybridization for atom: 0 -145: [03:35:40] UFFTYPER: Unrecognized atom type: Cu+1 (0) -145: .[03:35:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:35:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:35:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:35:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:35:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[03:35:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[03:35:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -145: ...[03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -145: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -159: file test5_2.png gave hash 2649140411U not the expected 97265124U -35: [03:35:40] ----------------------- -35: Testing isRingFused -147: [03:35:40] UFFTYPER: Unrecognized charge state for atom: 5 -159: file test5_3.png gave hash 2951986966U not the expected 606188176U -159: Done -159: ----------------- Test 6 (atom labels) -161: file rxn_test1_2.png gave hash 3312211595U not the expected 507435337U -147: [03:35:40] UFFTYPER: Unrecognized charge state for atom: 5 -124/238 Test #35: graphmolMolOpsTest ..................... Passed 2.99 sec +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [13:04:24] UFFTYPER: Unrecognized charge state for atom: 5 +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +147: [13:04:24] UFFTYPER: Unrecognized charge state for atom: 5 +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +161: ----------------- Test 1 +115: [13:04:24] 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: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +159: ----------------- Test 1 +68: Test +68: +68: mrtx1719_3d.mrv +68: +68: Test +68: +68: mrtx1719_atrop1.mrv +68: +68: Test +68: +68: mrtx1719_atrop2.mrv +68: +68: Test +68: +68: mrtx1719_atrop3.mrv +68: +68: Test +68: +68: mrtx1719_atropBad1.mrv +68: +68: [13:04:24] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +122/238 Test #139: pyMolTransforms ........................ Passed 1.29 sec +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. test 164 Start 164: pyFMCS 164: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/FMCS/Wrap/testFMCS.py" 164: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap 164: Test timeout computed to be: 1500 -159: Done -159: ----------------- Test 7 (backgrounds) -143: processing -143: launch :0 -143: launch :1 -143: [03:35:40] Rep: 0 Mol:0 -143: launch :2 -143: launch :3 -143: [03:35:40] Rep: 0 Mol:1 -143: [03:35:40] Rep: 0 Mol:5 -143: [03:35:40] Rep: 0 Mol:3 -143: [03:35:40] Rep: 0 Mol:9 -143: [03:35:40] Rep: 0 Mol:4 -159: file test7_1.png gave hash 2406197059U not the expected 1322246680U -143: [03:35:40] Rep: 0 Mol:13 -145: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -143: [03:35:40] Rep: 0 Mol:2 -159: file test7_2.png gave hash 4033628357U not the expected 1499012715U -143: [03:35:40] Rep: 0 Mol:17 -161: file rxn_test1_3.png gave hash 288594716U not the expected 1590809137U -159: Done -159: ----------------- Test8: PrepareMolDrawing -159: Done -159: ----------------- Test multi-threaded drawing -159: reading molecules -161: file rxn_test1_4.png gave hash 1996676260U not the expected 1766700542U -143: [03:35:40] Rep: 0 Mol:7 -160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U -154: .[03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -143: [03:35:40] Rep: 0 Mol:21 -143: [03:35:40] Rep: 0 Mol:11 -143: [03:35:40] Rep: 0 Mol:6 -143: [03:35:40] Rep: 0 Mol:25 -143: [03:35:40] Rep: 0 Mol:10 -143: [03:35:40] Rep: 0 Mol:15 -143: [03:35:40] Rep: 0 Mol:29 -161: file rxn_test1_5.png gave hash 1068409486U not the expected 2552100594U -154: .[03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -143: [03:35:40] Rep: 0 Mol:19 -160: file contourMol_2.svg gave hash 4241964660U not the expected 1815941817U -159: generating reference drawings -143: [03:35:40] Rep: 0 Mol:23 -143: [03:35:40] Rep: 0 Mol:27 -125: Warning: Atom Count for residue GLU53A does not match expected count -133: .............. -133: ---------------------------------------------------------------------- -133: Ran 14 tests in 0.160s -133: -133: OK -143: [03:35:40] Rep: 0 Mol:8 -143: [03:35:40] Rep: 0 Mol:31 -147: [03:35:40] UFFTYPER: Unrecognized charge state for atom: 6 -145: ... -145: ---------------------------------------------------------------------- -145: Ran 19 tests in 0.190s -145: -145: OK -160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U -143: [03:35:40] Rep: 0 Mol:14 -143: [03:35:40] Rep: 0 Mol:12 -161: file rxn_test1_6.png gave hash 1112775934U not the expected 3791582903U -147: [03:35:40] UFFTYPER: Unrecognized charge state for atom: 6 -160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U -143: [03:35:40] Rep: 0 Mol:18 -143: [03:35:40] Rep: 0 Mol:16 -160: file contourMol_5.svg gave hash 3954963517U not the expected 3792684719U -143: [03:35:40] Rep: 0 Mol:22 -147: [03:35:40] UFFTYPER: Unrecognized charge state for atom: 6 -98: . -98: ---------------------------------------------------------------------- -98: Ran 11 tests in 2.529s -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 0.08091020584106445 seconds -98: Skipped 10000000 in 0.8159685134887695 seconds -98: Skipped 10000000 in 0.563535213470459 seconds -143: [03:35:40] Rep: 0 Mol:26 -60: Test -60: -60: AtropCanon1.cxsmi -60: -60: Test -60: -60: AtropCanon2.cxsmi -60: -60: Test -60: -60: AtropCanon3.cxsmi -60: -60: Test -60: -60: BMS-986142_3d_chiral.cxsmi -60: -60: Test -60: -60: BMS-986142_3d.cxsmi -60: -60: =============================================================================== -60: All tests passed (2496 assertions in 31 test cases) -60: -125/238 Test #60: cxsmilesTest ........................... Passed 3.00 sec +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: .[13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[13:04:24] UFFTYPER: Unrecognized hybridization for atom: 0 +145: [13:04:24] UFFTYPER: Unrecognized atom type: Cu+1 (0) +145: .[13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +145: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: Elapsed time: 4.5616 s +115: Errors:0 +115: [13:04:24] test on : 500 molecules done +123/238 Test #115: testEEM ................................ Passed 4.63 sec test 165 Start 165: FMCStest 165: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 165: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test 165: Test timeout computed to be: 1500 -161: file rxn_test1_7.png gave hash 1360101162U not the expected 1461397406U -143: [03:35:40] Rep: 0 Mol:20 -143: [03:35:40] Rep: 0 Mol:30 -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 -156: . -156: ---------------------------------------------------------------------- -156: Ran 1 test in 0.065s -156: -156: OK -156: Testing Shape Helpers wrapper -143: [03:35:40] Rep: 0 Mol:24 +145: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +145: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +145: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +145: [13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[13:04:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +145: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +145: ...[13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +145: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +147: [13:04:24] UFFTYPER: Unrecognized charge state for atom: 5 +151: 107607411 +160: Randomness seeded to: 3389937298 +160: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U +124/238 Test #133: pyTestGenerator ........................ Passed 1.57 sec +test 166 + Start 166: molHashCatchTest + +166: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest +166: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash +166: Test timeout computed to be: 1500 +161: file rxn_test1_1.png gave hash 760679292U not the expected 801892091U +159: file test1_5.svg gave hash 2383324771U not the expected 2811480876U +159: Done +159: ----------------- Test 2 165: 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 @@ -27938,6 +27637,7 @@ 165: testChEMBL_Txt() chefopen 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 +89: [13:04:24] Explicit valence for atom # 3 Al, 6, is greater than permitted 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 @@ -28417,97 +28117,313 @@ 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 165: ERROR: RDKit could not load input file -126/238 Test #133: pyTestGenerator ........................ Passed 2.30 sec -127/238 Test #165: FMCStest ............................... Passed 0.04 sec -154: ..[03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -143: [03:35:40] Rep: 0 Mol:28 -161: file rxn_test2_1.png gave hash 3339775168U not the expected 3551633840U -test 166 - Start 166: molHashCatchTest - -166: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest -166: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash -166: Test timeout computed to be: 1500 +161: file rxn_test1_2.png gave hash 3312211595U not the expected 507435337U +125/238 Test #165: FMCStest ............................... Passed 0.10 sec test 167 Start 167: pyMolHash 167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolHash/Wrap/testMolHash.py" 167: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap 167: Test timeout computed to be: 1500 -154: .[03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[03:35:40] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -154: [03:35:40] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' -154: ... -154: ---------------------------------------------------------------------- -154: Ran 9 tests in 0.124s -154: -154: OK -158: . -158: ---------------------------------------------------------------------- -158: Ran 1 test in 0.011s -158: -158: OK +159: file test2_1.png gave hash 240594419U not the expected 638584804U +159: file test2_2.png gave hash 278647755U not the expected 610424244U +161: file rxn_test1_3.png gave hash 288594716U not the expected 1590809137U +160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U +126: Warning: Atom Count for residue GLU5A does not match expected count +145: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +160: file contourMol_2.svg gave hash 4241964660U not the expected 1815941817U +161: file rxn_test1_4.png gave hash 1996676260U not the expected 1766700542U +159: Done +159: ----------------- Test 4 +143: processing +143: launch :0 +143: launch :1 +143: launch :2 +143: [13:04:24] Rep: 0 Mol:1 +143: launch :3 +143: [13:04:24] Rep: 0 Mol:0 +143: [13:04:24] Rep: 0 Mol:3 +89: [13:04:24] Explicit valence for atom # 4 Al, 6, is greater than permitted +143: [13:04:24] Rep: 0 Mol:2 +143: [13:04:24] Rep: 0 Mol:5 +69: [13:04:24] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [13:04:24] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +143: [13:04:24] Rep: 0 Mol:9 +69: [13:04:24] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [13:04:24] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +143: [13:04:24] Rep: 0 Mol:4 +160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U +161: file rxn_test1_5.png gave hash 1068409486U not the expected 2552100594U +159: file test4_1.png gave hash 509333604U not the expected 3993974247U +159: Done +159: ----------------- Test 5 +69: [13:04:24] deprecated group abbreviation ignored on line 24 +143: [13:04:24] Rep: 0 Mol:8 +68: Test +68: +68: AlexRxn.mrv +68: +68: Test +68: +68: BadReactionSign.mrv +68: +68: Test +68: +68: bondArray_node.mrv +68: +68: Test +68: +68: marvin03.mrv +68: +68: Test +68: +68: marvin04.mrv +68: +68: Test +68: +68: marvin08.mrv +68: +68: Test +68: +68: marvin09.mrv +68: +68: Test +68: +68: marvin11.mrv +68: +68: Test +68: +68: marvin05.mrv +68: +68: Test +68: +68: EmptyRxn.mrv +68: +68: [13:04:24] initialization failed +143: [13:04:24] Rep: 0 Mol:13 +69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +69: [13:04:24] +69: +69: **** +69: Post-condition Violation +69: Element 'Mv' not found +69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +69: Failed Expression: anum > -1 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 3# 0x00007FAA724C8511 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x00007FAA724D1DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x00007FAA724D214D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 9# 0x00005654DCD6FC15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x00005654DCDD63F2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x00005654DCD56923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x00007FAA71A33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +69: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +69: 14# 0x00005654DCD56AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U 125: Warning: Atom Count for residue ARG64A does not match expected count -161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C -69: [03:35:40] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [03:35:40] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -128/238 Test #145: pyForceFieldHelpers .................... Passed 0.63 sec -160: file testGithub3226_1.png gave hash 2093087177U not the expected 3165135374U +159: file test5_1.png gave hash 650561118U not the expected 571291290U +89: [13:04:24] Explicit valence for atom # 10 Si, 6, is greater than permitted +160: file contourMol_5.svg gave hash 3954963517U not the expected 3792684719U +143: [13:04:24] Rep: 0 Mol:6 +147: [13:04:24] UFFTYPER: Unrecognized charge state for atom: 6 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +143: [13:04:24] Rep: 0 Mol:10 +143: [13:04:24] Rep: 0 Mol:12 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +159: file test5_2.png gave hash 2649140411U not the expected 97265124U +143: [13:04:24] Rep: 0 Mol:16 +143: [13:04:24] Rep: 0 Mol:17 +161: file rxn_test1_6.png gave hash 1112775934U not the expected 3791582903U +143: [13:04:24] Rep: 0 Mol:7 +143: [13:04:24] Rep: 0 Mol:11 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +147: [13:04:24] UFFTYPER: Unrecognized charge state for atom: 6 +148: ..[13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +143: [13:04:24] Rep: 0 Mol:15 +143: [13:04:24] Rep: 0 Mol:20 +143: [13:04:24] Rep: 0 Mol:19 +166: Randomness seeded to: 3795035291 +166: =============================================================================== +166: All tests passed (363 assertions in 14 test cases) +166: +159: file test5_3.png gave hash 2951986966U not the expected 606188176U +159: Done +159: ----------------- Test 6 (atom labels) +143: [13:04:24] Rep: 0 Mol:24 +126/238 Test #166: molHashCatchTest ....................... Passed 0.29 sec test 168 Start 168: testMMPA 168: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/testMMPA 168: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA 168: Test timeout computed to be: 1500 -159: processing -159: launch :0 -159: launch :1 -159: launch :2 -159: launch :3 +145: ... +145: ---------------------------------------------------------------------- +145: Ran 19 tests in 0.631s +145: +145: OK +143: [13:04:24] Rep: 0 Mol:23 +143: [13:04:24] Rep: 0 Mol:27 +143: [13:04:24] Rep: 0 Mol:28 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +143: [13:04:24] Rep: 0 Mol:21 +143: [13:04:24] Rep: 0 Mol:31 +161: file rxn_test1_7.png gave hash 1360101162U not the expected 1461397406U +159: Done +159: ----------------- Test 7 (backgrounds) +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +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 +143: [13:04:24] Rep: 0 Mol:25 +148: ..[13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +143: [13:04:24] Rep: 0 Mol:14 +161: file rxn_test2_1.png gave hash 3339775168U not the expected 3551633840U +147: [13:04:24] UFFTYPER: Unrecognized charge state for atom: 6 +159: file test7_1.png gave hash 2406197059U not the expected 1322246680U +143: [13:04:24] Rep: 0 Mol:18 +143: [13:04:24] Rep: 0 Mol:29 +148: .[13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +159: file test7_2.png gave hash 4033628357U not the expected 1499012715U +159: Done +159: ----------------- Test8: PrepareMolDrawing 161: file rxn_test2_2_1.png gave hash 457778262U not the expected 1268122583U -160: file testGithub3226_2.png gave hash 228776032U not the expected 643975155U -148: .[03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -129/238 Test #156: pyShapeHelpers ......................... Passed 0.45 sec -test 169 - Start 169: pyMMPA - -169: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/Wrap/testMMPA.py" -169: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap -169: Test timeout computed to be: 1500 +159: Done +159: ----------------- Test multi-threaded drawing +159: reading molecules 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 -130/238 Test #158: pyMolCatalog ........................... Passed 0.37 sec -test 170 - Start 170: testRascalMCES - -170: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES -170: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES -170: Test timeout computed to be: 1500 -160: file testGithub3226_3.png gave hash 1938488947U not the expected 3119571946U -161: file rxn_test2_2_2.png gave hash 4285088210U not the expected 82821108U -131/238 Test #98: pyChemReactionEnumerations ............. Passed 2.92 sec -test 171 - Start 171: testRascalCluster - -171: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster -171: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES -171: Test timeout computed to be: 1500 -160: file testPNGMetadata_1.png gave hash 3033029091U not the expected 997629701U -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 660865433U not the expected 3828365604U +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +143: [13:04:24] Rep: 0 Mol:22 +68: Test +68: +68: RxnNoCoords.mrv +68: +68: Test +68: +68: mrvValenceZero.mrv +68: +68: Test +68: +68: condition_coordinates_mpoint.mrv +68: +68: Test +68: +68: marvin01.mrv +68: +68: Test +68: +68: aspirineSynthesisWithAttributes.mrv +68: +68: Test +68: +68: marvin01.mrv +68: +68: Test +68: +68: NewChiralTest +68: +68: Test +68: +68: NewChiralTest +68: +68: Test +68: +68: NewChiralTestNoChiral +68: +68: Test +68: +68: NewChiralTestNoChiral +68: +68: Test +68: +68: NewChiralTest2 +68: +68: Test +68: +68: NewChiralTest2 +68: +68: Test +68: +68: NewChiralTest2AllChiral +68: +68: Test +68: +68: NewChiralTest2AllChiral +68: +68: Test +68: +68: Vendor839 +68: +68: Test +68: +68: DoubleBondChain +68: +68: Test +68: +68: Na_Mg_Al_OH +68: +68: Test +68: +68: Pb +68: +68: Test +68: +68: O_Mg_Si +68: +68: Test +68: +68: SquiggleBond +68: +68: Test +68: +68: BigMacrocycle +68: +68: Test +68: +68: Smiles1 +68: +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.005215 seconds +168: Time elapsed 0.013039 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. +143: [13:04:24] Rep: 0 Mol:26 168: 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. +127/238 Test #68: testMrvToMol ........................... Passed 5.79 sec +test 169 + Start 169: pyMMPA + +169: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MMPA/Wrap/testMMPA.py" +169: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap +169: Test timeout computed to be: 1500 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() 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. -69: [03:35:40] Empty atom list: 'M ALS 1 0 F' on line 8. 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] @@ -28516,19 +28432,21 @@ 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. -69: de_DE.UTF-8 +141: processing +141: launch :0 +141: [13:04:24] Rep: 0 Mol:0 +141: launch :1 +141: launch :2 +141: launch :3 +141: [13:04:24] [13:04:24] Rep: 0 Mol:1 168: 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. -69: [03:35:40] ------------------------------------- -132/238 Test #154: pyChemicalFeatures ..................... Passed 0.52 sec +161: file rxn_test2_2_2.png gave hash 4285088210U not the expected 82821108U 168: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 168: 10: NOREF. Reference data NOT LISTED in test case. -test 172 - Start 172: pyRascalMCES - -172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" -172: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap -172: Test timeout computed to be: 1500 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:24] Rep: 0 Mol:5 +141: [13:04:24] Rep: 0 Mol:3 168: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 168: 11: NOREF. Reference data NOT LISTED in test case. 168: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] @@ -28539,71 +28457,106 @@ 168: 14: NOREF. Reference data NOT LISTED in test case. 168: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 168: 15: NOREF. Reference data NOT LISTED in test case. +141: Rep: 0 Mol:2 +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 +130: [13:04:24] done +130: [13:04:24] ------------------------------------- +130: [13:04:24] Test Rooted Topological Torsions. +130: [13:04:24] done +130: [13:04:24] ------------------------------------- +130: [13:04:24] Test ignoring atoms in Topological Torsions. +130: [13:04:24] done +130: [13:04:24] ------------------------------------- +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:24] Rep: 0 Mol:9 168: 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. -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 -69: [03:35:40] Test multithreading Locale Switching 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 1904681261U not the expected 1230108677U -161: Done -161: ----------------- Test 3: test reactant highlighting +130: [13:04:24] ------------------------------------- +130: [13:04:24] Test Topological Torsions including info about chirality. +130: [13:04:24] done +130: [13:04:24] ------------------------------------- +130: [13:04:24] Test GitHub Issue 25: fingerprint backwards compatibility. +143: [13:04:24] Rep: 0 Mol:30 +130: [13:04:24] done +130: [13:04:24] ------------------------------------- +130: [13:04:24] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +130: [13:04:24] done +130: [13:04:24] ------------------------------------- +130: [13:04:24] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +141: [13:04:24] Rep: 0 Mol:4 +161: file rxn_test2_2_3.png gave hash 660865433U not the expected 3828365604U +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +130: [13:04:24] done +130: [13:04:24] ------------------------------------- +130: [13:04:24] Test convenience and bulk fp calculation functions +159: generating reference drawings +141: [13:04:24] Rep: 0 Mol:13 +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 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() 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 0.004306 seconds +168: Time elapsed 0.012401 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 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:24] Rep: 0 Mol:17 168: 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] 168: 3: PASSED. matchedRefRes = 6 168: 4: O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OC[*:2] 168: 4: PASSED. matchedRefRes = 13 -160: file testPNGMetadata_2.png gave hash 2637596984U not the expected 1797853056U +161: file rxn_test2_2_4.png gave hash 1904681261U not the expected 1230108677U 168: 5: O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].O[*:2] 168: 5: PASSED. matchedRefRes = 12 +160: file testGithub3226_1.png gave hash 2093087177U not the expected 3165135374U 168: 6: NULL, Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 168: 6: PASSED. matchedRefRes = 10 +141: [13:04:24] Rep: 0 Mol:8 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +161: Done +161: ----------------- Test 3: test reactant highlighting 168: 7: O=C(N[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case.O=C(N[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 8: O=C(NC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 8: NOREF. Reference data NOT LISTED in test case.O=C(NC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 9: O=C(NCC[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 9: NOREF. Reference data NOT LISTED in test case.O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() 168: 10: NULL, Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 10: PASSED. matchedRefRes = 3 168: 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] +141: [13:04:24] Rep: 0 Mol:6 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:24] Rep: 0 Mol:12 168: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 12: PASSED. matchedRefRes = 8 -141: processing -141: launch :0 -141: launch :1 168: 13: NULL, Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 13: PASSED. matchedRefRes = 9 -141: launch :2 -141: [03:35:40] Rep: 0 Mol:1 -141: launch :3 -141: [03:35:40] Rep: 0 Mol:2 -141: [03:35:40] Rep: 0 Mol:0 168: 14: C([*:1])[*:2], Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 14: PASSED. matchedRefRes = 11 168: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 15: PASSED. matchedRefRes = 2 -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:35:40] Rep: 0 Mol:5 -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:35:40] Rep: 0 Mol:9 -141: [03:35:40] Rep: 0 Mol:3 -161: file rxn_test3_1.png gave hash 786828249U not the expected 4189980366U -148: ..[03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:24] Rep: 0 Mol:10 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:24] Rep: 0 Mol:16 +160: file testGithub3226_2.png gave hash 228776032U not the expected 643975155U +141: [13:04:24] Rep: 0 Mol:7 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:24] Rep: 0 Mol:11 +141: [13:04:24] Rep: 0 Mol:15 168: 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] @@ -28613,64 +28566,73 @@ 168: ----------------------------------- 168: 168: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -168: Time elapsed 0.004176 seconds +168: Time elapsed 0.011319 seconds 168: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 168: 1: PASSED. matchedRefRes = 4 +89: [13:04:24] Explicit valence for atom # 2 O, 4, is greater than permitted +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() 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 -130: [03:35:40] done -130: [03:35:40] ------------------------------------- -130: [03:35:40] Test GitHub Issue #6958 168: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2] 168: 4: PASSED. matchedRefRes = 13 -130: [03:35:40] DEPRECATION WARNING: please use AtomPairGenerator +141: [13:04:24] Rep: 0 Mol:21 +141: [13:04:24] Rep: 0 Mol:20 168: 5: res= O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].O[*:2] 168: 5: PASSED. matchedRefRes = 12 +141: [13:04:24] Rep: 0 Mol:19 +161: file rxn_test3_1.png gave hash 786828249U not the expected 4189980366U 168: 6: res= NULL,Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 168: 6: PASSED. matchedRefRes = 10 -161: Done -161: ----------------- Test 4: some examples from SMARTS in testing -161: draw! +160: file testGithub3226_3.png gave hash 1938488947U not the expected 3119571946U +89: [13:04:24] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [13:04:24] Explicit valence for atom # 3 Be, 4, is greater than permitted 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. -69: [03:35:40] Test multithreading (Done) -69: [03:35:40] ------------------------------------- -133/238 Test #130: testFingerprintGenerators .............. Passed 2.57 sec -test 173 - Start 173: testSynthonSpaceSubstructureSearch - -173: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch -173: Test timeout computed to be: 1500 -141: [03:35:40] Rep: 0 Mol:13 -141: [03:35:40] Rep: 0 Mol:4 -162: ...[03:35:40] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -162: [03:35:40] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 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. +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() 168: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 168: 10: PASSED. matchedRefRes = 3 +141: [13:04:24] Rep: 0 Mol:23 +141: [13:04:24] Rep: 0 Mol:27 168: 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. +128/238 Test #145: pyForceFieldHelpers .................... Passed 1.83 sec +test 170 + Start 170: testRascalMCES + +170: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES +170: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES +170: Test timeout computed to be: 1500 +161: Done +161: ----------------- Test 4: some examples from SMARTS in testing 168: 12: res= C(C[*:2])[*:1],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 12: PASSED. matchedRefRes = 8 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +161: draw! 168: 13: res= NULL,Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:1] 168: 13: PASSED. matchedRefRes = 9 +141: [13:04:24] Rep: 0 Mol:25 +141: [13:04:24] Rep: 0 Mol:24 168: 14: res= C([*:1])[*:2],Cc1c(C(=O)NC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] 168: 14: PASSED. matchedRefRes = 11 168: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 168: 15: PASSED. matchedRefRes = 2 -117: =>start test AUTOCORR3D custom -117: [03:35:40] test on : 365 molecules done -166: Randomness seeded to: 998955042 -166: =============================================================================== -166: All tests passed (363 assertions in 14 test cases) -166: -134/238 Test #166: molHashCatchTest ....................... Passed 0.14 sec +141: [13:04:24] Rep: 0 Mol:31 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +160: file testPNGMetadata_1.png gave hash 3033029091U not the expected 997629701U +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:24] Rep: 0 Mol:29 +154: .[13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:24] Rep: 0 Mol:28 +89: [13:04:24] Explicit valence for atom # 27 P, 6, is greater than permitted 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] @@ -28680,7 +28642,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -168: Time elapsed 0.001157 seconds +168: Time elapsed 0.001127 seconds 168: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 168: 1: PASSED. matchedRefRes = 2 168: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] @@ -28691,16 +28653,12 @@ 168: 4: PASSED. matchedRefRes = 4 168: 5: res= NULL,C1CN1[*:1].CC(C=O)[*:1] 168: 5: PASSED. matchedRefRes = 5 -test 174 - Start 174: testSynthonSpaceRascalSearch - -174: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceRascalSearch -174: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch -174: 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: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] 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] @@ -28708,33 +28666,25 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.006239 seconds +168: Time elapsed 0.024878 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. +69: [13:04:24] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: [13:04:24] 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: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +161: file rxn_test4_1.png gave hash 1704194173U not the expected 2745201873U 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. 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] 168: 6: NOREF. Reference data NOT LISTED in test case. -69: *************************************** -69: *************************************** -141: [03:35:40] Rep: 0 Mol:17 168: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 168: 7: NOREF. Reference data NOT LISTED in test case. -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() 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. 168: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] @@ -28743,54 +28693,63 @@ 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 168: 11: NOREF. Reference data NOT LISTED in test case. -141: [03:35:40] Rep: 0 Mol:8 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:24] Rep: 0 Mol:14 168: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 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_test4_1.png gave hash 1704194173U not the expected 2745201873U -69: [03:35:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -69: [03:35:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 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: done 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. +89: =============================================================================== +89: All tests passed (21562 assertions in 3 test cases) +89: 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. +129/238 Test #89: multithreadedSupplierCatchTest ......... Passed 5.85 sec +test 171 + Start 171: testRascalCluster + +171: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster +171: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES +171: Test timeout computed to be: 1500 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:35:40] Rep: 0 Mol:12 -161: done +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() 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 0.004958 seconds +168: Time elapsed 0.013067 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. 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. +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() 168: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1 168: 4: NOREF. Reference data NOT LISTED in test case. +141: [13:04:24] Rep: 0 Mol:18 168: 5: res= O=C(O[*:1])C([*:2])[*:3],O[*:2].c1ccc(C[*:1])cc1.c1ccc([*:3])cc1 168: 5: NOREF. Reference data NOT LISTED in test case. 168: 6: res= O=C(O[*:1])C(O)[*:2],c1ccc(C[*:1])cc1.c1ccc([*:2])cc1 168: 6: NOREF. Reference data NOT LISTED in test case. -141: [03:35:40] Rep: 0 Mol:16 168: 7: res= NULL,O=C(OC[*:1])C(O)c1ccccc1.c1ccc([*:1])cc1 168: 7: NOREF. Reference data NOT LISTED in test case. 168: 8: res= O=C(OC[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc([*:2])cc1 168: 8: NOREF. Reference data NOT LISTED in test case. -148: ..[03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() 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: [13:04:24] 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 @@ -28799,36 +28758,128 @@ 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. -141: [03:35:40] Rep: 0 Mol:7 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +160: file testPNGMetadata_2.png gave hash 2637596984U not the expected 1797853056U 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. -69: [03:35:40] bond with order 0 found on line 7. This is not part of the MDL specification. 168: 16: res= NULL,O=C(OCc1ccccc1)C(c1ccccc1)[*:1].O[*:1] 168: 16: NOREF. Reference data NOT LISTED in test case. 168: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 168: 17: NOREF. Reference data NOT LISTED in test case. -141: [03:35:40] Rep: 0 Mol:6 168: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 168: 18: NOREF. Reference data NOT LISTED in test case. -141: [03:35:40] Rep: 0 Mol:11 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:24] Rep: 0 Mol:22 168: 168: --- ALL PASSED --- 168: ----------------------------------- 168: 5 TEST CASES FAILED -162: ..........[03:35:40] -162: -162: **** -135/238 Test #168: testMMPA ............................... Passed 0.17 sec -141: [03:35:40] Rep: 0 Mol:10 +130/238 Test #168: testMMPA ............................... Passed 0.52 sec +125: Warning: Atom Count for residue LYS80A does not match expected count +test 172 + Start 172: pyRascalMCES + +172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" +172: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap +172: Test timeout computed to be: 1500 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +156: . +156: ---------------------------------------------------------------------- +156: Ran 1 test in 0.192s +156: +156: OK +156: Testing Shape Helpers wrapper +161: file rxn_test4_2.png gave hash 30753303U not the expected 3094925886U +141: [13:04:24] Rep: 0 Mol:26 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +159: processing +159: launch :0 +159: launch :1 +158: . +158: ---------------------------------------------------------------------- +158: Ran 1 test in 0.048s +158: +158: OK +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +161: Done +159: launch :2 +159: launch :3 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +131/238 Test #161: moldraw2DRxnTest1 ...................... Passed 1.00 sec +test 173 + Start 173: testSynthonSpaceSubstructureSearch + +173: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch +173: Test timeout computed to be: 1500 +141: [13:04:24] Rep: 0 Mol:30 +148: [13:04:24] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:25] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:25] Molecule does not have explicit Hs. Consider calling AddHs() +117: =>start test morse custom +117: [13:04:25] test on : 365 molecules done +154: ..[13:04:25] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:04:25] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[13:04:25] Molecule does not have explicit Hs. Consider calling AddHs() +132/238 Test #156: pyShapeHelpers ......................... Passed 1.22 sec +test 174 + Start 174: testSynthonSpaceRascalSearch + +174: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceRascalSearch +174: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch +174: Test timeout computed to be: 1500 +154: .[13:04:25] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +154: [13:04:25] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +154: ... +154: ---------------------------------------------------------------------- +154: Ran 9 tests in 0.404s +154: +154: OK +162: ...[13:04:25] Font file /build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +162: [13:04:25] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +167: .... +167: ---------------------------------------------------------------------- +167: Ran 4 tests in 0.043s +167: +167: OK +69: ---------------------------------- +69: ---------------------------------- +133/238 Test #158: pyMolCatalog ........................... Passed 1.26 sec test 175 Start 175: testCIPLabeler 175: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 175: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler 175: Test timeout computed to be: 1500 -141: [03:35:40] Rep: 0 Mol:20 +69: [13:04:25] +69: +69: **** +69: Pre-condition Violation +69: rlabel out of range for MDL files +69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp +69: Failed Expression: rlabel >= 0 && rlabel < 100 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +69: 3# 0x00005654DCD7CFFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x00005654DCDD646A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x00005654DCD56923 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x00007FAA71A33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +69: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +69: 8# 0x00005654DCD56AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +69: [13:04:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +162: ..........[13:04:25] +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 @@ -28840,7 +28891,7 @@ 162: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/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-202503.1/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# 0x00007FB650DDF62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +162: 5# 0x00007F06BEEDF62C 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-202503.1/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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -28851,17 +28902,17 @@ 162: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-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-202503.1/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-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 16# 0x00007FB64FFB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 17# 0x00007FB64FFB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 18# 0x00007FB64FFB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 19# 0x00007FB64FFB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -162: 20# 0x00007FB64FFB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 16# 0x00007F06BD3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 17# 0x00007F06BD3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 18# 0x00007F06BD3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 19# 0x00007F06BD3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +162: 20# 0x00007F06BD3B7933 in /build/reproducible-path/rdkit-202503.1/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-202503.1/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-202503.1/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-202503.1/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-202503.1/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# 0x00007FB650DDC3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +162: 26# 0x00007F06BEEDC3C6 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# 0x00000000005CBA19 in /usr/bin/python3 @@ -28893,398 +28944,467 @@ 162: 55# 0x00000000006B339E in /usr/bin/python3 162: 56# Py_RunMain in /usr/bin/python3 162: 57# Py_BytesMain in /usr/bin/python3 -162: 58# 0x00007FB652BECCA8 in /lib/x86_64-linux-gnu/libc.so.6 +162: 58# 0x00007F06C00F5CA8 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: -141: [03:35:40] Rep: 0 Mol:15 -141: [03:35:40] Rep: 0 Mol:19 -148: .[03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:35:40] Rep: 0 Mol:23 -141: [03:35:40] Rep: 0 Mol:21 -141: [03:35:40] Rep: 0 Mol:27 -141: [03:35:40] Rep: 0 Mol:24 -69: [03:35:40] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -69: [03:35:40] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -69: [03:35:40] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -141: [03:35:40] Rep: 0 Mol:31 -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:35:40] Rep: 0 Mol:25 -141: [03:35:40] Rep: 0 Mol:28 -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:35:40] Rep: 0 Mol:29 -175: Randomness seeded to: 1408828776 -175: [03:35:40] non kekulizable aromatic bond being treated as bond order 1 -175: [03:35:40] non kekulizable aromatic bond being treated as bond order 1 -175: [03:35:40] non kekulizable aromatic bond being treated as bond order 1 -175: [03:35:40] non kekulizable aromatic bond being treated as bond order 1 -175: [03:35:40] non kekulizable aromatic bond being treated as bond order 1 -175: [03:35:40] non kekulizable aromatic bond being treated as bond order 1 -69: generating smiles -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -69: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -69: converting back -161: file rxn_test4_2.png gave hash 30753303U not the expected 3094925886U -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -160: [03:35:40] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:35:40] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -161: Done -69: check isomorphism -136/238 Test #161: moldraw2DRxnTest1 ...................... Passed 0.50 sec +160: [13:04:25] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [13:04:25] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +148: [13:04:25] Molecule does not have explicit Hs. Consider calling AddHs() +160: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U +141: [13:04:25] Rep: 20 Mol:3 +160: [13:04:25] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [13:04:25] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +141: [13:04:25] Rep: 20 Mol:7 +141: [13:04:25] Rep: 20 Mol:11 +141: [13:04:25] Rep: 20 Mol:15 +141: [13:04:25] Rep: 20 Mol:19 +141: [13:04:25] Rep: 20 Mol:23 +141: [13:04:25] Rep: 20 Mol:27 +141: [13:04:25] Rep: 20 Mol:31 +148: [13:04:25] Molecule does not have explicit Hs. Consider calling AddHs() +175: Randomness seeded to: 4196802469 +175: [13:04:25] non kekulizable aromatic bond being treated as bond order 1 +175: [13:04:25] non kekulizable aromatic bond being treated as bond order 1 +175: [13:04:25] non kekulizable aromatic bond being treated as bond order 1 +175: [13:04:25] non kekulizable aromatic bond being treated as bond order 1 +175: [13:04:25] non kekulizable aromatic bond being treated as bond order 1 +175: [13:04:25] non kekulizable aromatic bond being treated as bond order 1 +134/238 Test #154: pyChemicalFeatures ..................... Passed 1.54 sec test 176 Start 176: pyCIPLabelsWrapTest 176: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" 176: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 176: Test timeout computed to be: 1500 -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: Warning: Atom Count for residue LYS80A does not match expected count -126: Warning: Atom Count for residue ASN39A does not match expected count -160: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U -160: [03:35:40] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:35:40] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:35:40] Rep: 0 Mol:14 -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -160: file testHandDrawn-1.png gave hash 70252907U not the expected 3894611804U -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -108: .............[03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -108: [03:35:40] SMILES Parse Error: syntax error while parsing: --- -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] --- -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [03:35:40] dasfsadf -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:35:40] Rep: 0 Mol:18 -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -89: [03:35:40] Explicit valence for atom # 9 N, 5, is greater than permitted -162: ...................... -162: ---------------------------------------------------------------------- -162: Ran 35 tests in 0.266s -162: -162: OK -162: json lasso -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -175: [03:35:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -175: [03:35:40] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:35:40] Rep: 0 Mol:22 -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -117: =>start test 2 WHIM custom -117: [03:35:40] test on : 365 molecules done -141: [03:35:40] Rep: 0 Mol:26 -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -160: [03:35:40] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:35:40] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -175: =============================================================================== -175: All tests passed (6577 assertions in 19 test cases) -175: -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -137/238 Test #175: testCIPLabeler ......................... Passed 0.23 sec +141: [13:04:25] Rep: 20 Mol:0 +141: [13:04:25] Rep: 20 Mol:4 +141: [13:04:25] Rep: 20 Mol:8 +141: [13:04:25] Rep: 20 Mol:12 +141: [13:04:25] Rep: 20 Mol:16 +141: [13:04:25] Rep: 20 Mol:20 +135/238 Test #167: pyMolHash .............................. Passed 1.16 sec test 177 Start 177: pyCIPLabelsValidation 177: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 177: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 177: Test timeout computed to be: 1500 -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:25] Rep: 20 Mol:24 +141: [13:04:25] Rep: 20 Mol:28 +141: [13:04:25] Rep: 20 Mol:1 +141: [13:04:25] Rep: 20 Mol:5 +141: [13:04:25] Rep: 20 Mol:9 +141: [13:04:25] Rep: 20 Mol:13 +141: [13:04:25] Rep: 20 Mol:17 +141: [13:04:25] Rep: 20 Mol:21 +141: [13:04:25] Rep: 20 Mol:25 +141: [13:04:25] Rep: 20 Mol:29 +160: file testHandDrawn-1.png gave hash 70252907U not the expected 3894611804U +148: [13:04:25] Molecule does not have explicit Hs. Consider calling AddHs() +126: Warning: Atom Count for residue ASN39A does not match expected count +160: [13:04:25] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [13:04:25] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +148: [13:04:25] Molecule does not have explicit Hs. Consider calling AddHs() 160: file testHandDrawn-2.svg gave hash 1534109833U not the expected 794717511U -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -160: [03:35:40] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:35:40] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:35:40] Rep: 0 Mol:30 +160: [13:04:25] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [13:04:25] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +162: ...................... +162: ---------------------------------------------------------------------- +162: Ran 35 tests in 0.509s +162: +162: OK +162: json lasso +148: [13:04:25] Molecule does not have explicit Hs. Consider calling AddHs() 160: file testHandDrawn-2.png gave hash 4273438430U not the expected 1443443188U -160: [03:35:40] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:35:40] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: [13:04:25] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [13:04:25] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. 160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U -138/238 Test #162: pyMolDraw2D ............................ Passed 0.67 sec +160: [13:04:25] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [13:04:25] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +136/238 Test #162: pyMolDraw2D ............................ Passed 1.65 sec test 178 Start 178: deprotectTest 178: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 178: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect 178: Test timeout computed to be: 1500 -160: [03:35:40] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:35:40] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +108: .............[13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +148: [13:04:25] Molecule does not have explicit Hs. Consider calling AddHs() +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf +108: [13:04:25] SMILES Parse Error: syntax error while parsing: --- +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] --- +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [13:04:25] dasfsadf 160: file testHandDrawn-3.png gave hash 258221924U not the expected 865629432U -160: [03:35:40] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:35:40] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: [13:04:25] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [13:04:25] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +141: [13:04:25] Rep: 40 Mol:3 160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U -160: [03:35:40] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:35:40] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +160: [13:04:25] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [13:04:25] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +141: [13:04:25] Rep: 40 Mol:7 +141: [13:04:25] Rep: 40 Mol:11 +141: [13:04:25] Rep: 40 Mol:15 +141: [13:04:25] Rep: 40 Mol:19 +141: [13:04:25] Rep: 40 Mol:23 +141: [13:04:25] Rep: 40 Mol:27 +141: [13:04:25] Rep: 40 Mol:31 160: file testHandDrawn-4.png gave hash 2602629668U not the expected 3919767093U -143: [03:35:40] Rep: 100 Mol:3 -143: [03:35:40] Rep: 100 Mol:7 -143: [03:35:40] Rep: 100 Mol:11 -143: [03:35:40] Rep: 100 Mol:15 -143: [03:35:40] Rep: 100 Mol:19 -143: [03:35:40] Rep: 100 Mol:23 -143: [03:35:40] Rep: 100 Mol:27 -143: [03:35:40] Rep: 100 Mol:31 -141: [03:35:40] Rep: 20 Mol:3 -141: [03:35:40] Rep: 20 Mol:7 -141: [03:35:40] Rep: 20 Mol:11 -141: [03:35:40] Rep: 20 Mol:15 -141: [03:35:40] Rep: 20 Mol:19 -141: [03:35:40] Rep: 20 Mol:23 -141: [03:35:40] Rep: 20 Mol:27 -141: [03:35:40] Rep: 20 Mol:31 -141: [03:35:40] Rep: 20 Mol:0 -141: [03:35:40] Rep: 20 Mol:4 -141: [03:35:40] Rep: 20 Mol:8 -141: [03:35:40] Rep: 20 Mol:12 -141: [03:35:40] Rep: 20 Mol:16 -141: [03:35:40] Rep: 20 Mol:20 -141: [03:35:40] Rep: 20 Mol:24 -141: [03:35:40] Rep: 20 Mol:28 -167: .... -167: ---------------------------------------------------------------------- -167: Ran 4 tests in 0.015s -167: -167: OK -108: .[03:35:40] SMILES Parse Error: syntax error while parsing: mydoghasfleas -108: [03:35:40] SMILES Parse Error: check for mistakes around position 1: -108: [03:35:40] mydoghasfleas -108: [03:35:40] ^ -108: [03:35:40] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -139/238 Test #167: pyMolHash .............................. Passed 0.50 sec +141: [13:04:25] Rep: 20 Mol:2 +141: [13:04:25] Rep: 20 Mol:6 +141: [13:04:25] Rep: 20 Mol:10 +141: [13:04:25] Rep: 20 Mol:14 +141: [13:04:25] Rep: 20 Mol:18 +141: [13:04:25] Rep: 20 Mol:22 +141: [13:04:25] Rep: 20 Mol:26 +143: [13:04:25] Rep: 100 Mol:3 +143: [13:04:25] Rep: 100 Mol:7 +143: [13:04:25] Rep: 100 Mol:11 +143: [13:04:25] Rep: 100 Mol:15 +143: [13:04:25] Rep: 100 Mol:19 +143: [13:04:25] Rep: 100 Mol:23 +143: [13:04:25] Rep: 100 Mol:27 +143: [13:04:25] Rep: 100 Mol:31 +141: [13:04:25] Rep: 20 Mol:30 +175: [13:04:25] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +175: [13:04:25] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +148: [13:04:25] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:25] Rep: 40 Mol:1 +141: [13:04:25] Rep: 40 Mol:5 +141: [13:04:25] Rep: 40 Mol:9 +141: [13:04:25] Rep: 40 Mol:13 +141: [13:04:25] Rep: 40 Mol:17 +141: [13:04:25] Rep: 40 Mol:21 +141: [13:04:25] Rep: 40 Mol:0 +141: [13:04:25] Rep: 40 Mol:25 +141: [13:04:25] Rep: 40 Mol:4 +141: [13:04:25] Rep: 40 Mol:29 +141: [13:04:25] Rep: 40 Mol:8 +141: [13:04:25] Rep: 40 Mol:12 +141: [13:04:25] Rep: 40 Mol:16 126: Warning: Atom Count for residue GLU53A does not match expected count +60: Test +60: +60: AtropCanon1.cxsmi +60: +60: Test +60: +60: AtropCanon2.cxsmi +60: +60: Test +60: +60: AtropCanon3.cxsmi +60: +60: Test +60: +60: BMS-986142_3d_chiral.cxsmi +60: +60: Test +60: +60: BMS-986142_3d.cxsmi +60: +60: =============================================================================== +60: All tests passed (2496 assertions in 31 test cases) +60: +141: [13:04:25] Rep: 40 Mol:20 +137/238 Test #60: cxsmilesTest ........................... Passed 7.33 sec test 179 Start 179: pyDeprotect 179: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Deprotect/Wrap/rough_test.py" 179: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap 179: Test timeout computed to be: 1500 -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -172: ..........[03:35:40] Too many matching bond pairs (1032) so can't continue. -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:35:40] Rep: 20 Mol:1 -141: [03:35:40] Rep: 20 Mol:5 -141: [03:35:40] Rep: 20 Mol:9 -141: [03:35:40] Rep: 20 Mol:13 -141: [03:35:40] Rep: 20 Mol:17 -89: [03:35:40] Explicit valence for atom # 3 Al, 6, is greater than permitted -141: [03:35:40] Rep: 20 Mol:21 -141: [03:35:40] Rep: 20 Mol:25 -141: [03:35:40] Rep: 20 Mol:29 -122: =>start test GETAWAY -122: [03:35:40] test on : 365 molecules done -126: Warning: Atom Count for residue ARG64A does not match expected count -140/238 Test #122: testGETAWAY ............................ Passed 3.20 sec +141: [13:04:25] Rep: 40 Mol:24 +141: [13:04:25] Rep: 40 Mol:28 +148: [13:04:25] Molecule does not have explicit Hs. Consider calling AddHs() +178: Randomness seeded to: 2572402508 +178: =============================================================================== +178: All tests passed (111 assertions in 3 test cases) +178: +108: .[13:04:25] SMILES Parse Error: syntax error while parsing: mydoghasfleas +108: [13:04:25] SMILES Parse Error: check for mistakes around position 1: +108: [13:04:25] mydoghasfleas +108: [13:04:25] ^ +108: [13:04:25] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +175: =============================================================================== +175: All tests passed (6577 assertions in 19 test cases) +175: +138/238 Test #178: deprotectTest .......................... Passed 0.34 sec test 180 Start 180: testReducedGraphs -180: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs -180: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs -180: Test timeout computed to be: 1500 +180: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs +180: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs +180: Test timeout computed to be: 1500 +139/238 Test #175: testCIPLabeler ......................... Passed 0.82 sec +test 181 + Start 181: pyReducedGraphs + +181: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" +181: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap +181: Test timeout computed to be: 1500 +143: [13:04:26] Rep: 100 Mol:0 +143: [13:04:26] Rep: 100 Mol:4 +143: [13:04:26] Rep: 100 Mol:8 +143: [13:04:26] Rep: 100 Mol:12 +143: [13:04:26] Rep: 100 Mol:16 +143: [13:04:26] Rep: 100 Mol:20 +143: [13:04:26] Rep: 100 Mol:24 +143: [13:04:26] Rep: 100 Mol:28 +143: [13:04:26] Rep: 100 Mol:1 +143: [13:04:26] Rep: 100 Mol:5 +143: [13:04:26] Rep: 100 Mol:9 +143: [13:04:26] Rep: 100 Mol:13 +143: [13:04:26] Rep: 100 Mol:17 +143: [13:04:26] Rep: 100 Mol:21 +143: [13:04:26] Rep: 100 Mol:25 +143: [13:04:26] Rep: 100 Mol:29 +130: [13:04:26] done +130: [13:04:26] ------------------------------------- +130: [13:04:26] Test GitHub Issue #6958 +130: [13:04:26] DEPRECATION WARNING: please use AtomPairGenerator +176: .... +176: ---------------------------------------------------------------------- +176: Ran 4 tests in 0.038s +176: +176: OK +140/238 Test #130: testFingerprintGenerators .............. Passed 3.66 sec +test 182 + Start 182: trajectoryTest + +182: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest +182: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory +182: Test timeout computed to be: 1500 +148: [13:04:26] Molecule does not have explicit Hs. Consider calling AddHs() +180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] +180: +180: 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, ] +180: +180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, ] +180: +180: 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, ] +180: +69: [13:04:26] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [13:04:26] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +180: 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, ] +180: +180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] +180: +141: [13:04:26] Rep: 60 Mol:3 +141: [13:04:26] Rep: 60 Mol:7 +141: [13:04:26] Rep: 60 Mol:11 +141: [13:04:26] Rep: 60 Mol:15 +141: [13:04:26] Rep: 60 Mol:19 +141: [13:04:26] Rep: 60 Mol:23 +141: [13:04:26] Rep: 60 Mol:27 +141: [13:04:26] Rep: 60 Mol:31 +180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 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, 0.3, 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, 0.3, 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, ] +180: +180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 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, 0.3, 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, 0.3, 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, ] +180: +180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] +180: +148: [13:04:26] Molecule does not have explicit Hs. Consider calling AddHs() +141/238 Test #180: testReducedGraphs ...................... Passed 0.20 sec +test 183 + Start 183: substructLibraryTest + +183: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest +183: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary +183: Test timeout computed to be: 1500 +142/238 Test #176: pyCIPLabelsWrapTest .................... Passed 0.89 sec +test 184 + Start 184: substructLibraryCatchTest + +184: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest +184: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary +184: Test timeout computed to be: 1500 +148: [13:04:26] Molecule does not have explicit Hs. Consider calling AddHs() +183: [13:04:26] ------------------------------------- +183: [13:04:26] Test1 +126: Warning: Atom Count for residue ARG64A does not match expected count +148: [13:04:26] Molecule does not have explicit Hs. Consider calling AddHs() +69: [13:04:26] Empty atom list: 'M ALS 1 0 F' on line 8. 108: ....... 108: ---------------------------------------------------------------------- -108: Ran 21 tests in 3.077s +108: Ran 21 tests in 3.864s 108: 108: OK 108: (Five aromatic carbons And (Not any of Five aromatic carbons)) @@ -29306,138 +29426,222 @@ 108: 1 108: 2 108: running -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:35:40] Rep: 40 Mol:3 -141: [03:35:40] Rep: 40 Mol:7 -178: Randomness seeded to: 2367443123 -178: =============================================================================== -178: All tests passed (111 assertions in 3 test cases) -178: -141: [03:35:40] Rep: 40 Mol:11 -141: [03:35:40] Rep: 40 Mol:15 -141: [03:35:40] Rep: 40 Mol:19 -141: [03:35:40] Rep: 40 Mol:23 -141: [03:35:40] Rep: 40 Mol:27 -141: [03:35:40] Rep: 40 Mol:31 -141/238 Test #178: deprotectTest .......................... Passed 0.23 sec -test 181 - Start 181: pyReducedGraphs +148: [13:04:26] Molecule does not have explicit Hs. Consider calling AddHs() +69: de_DE.UTF-8 +69: [13:04:26] ------------------------------------- +69: [13:04:26] Test multithreading Locale Switching +141: [13:04:26] Rep: 60 Mol:1 +148: [13:04:26] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:26] Rep: 60 Mol:5 +141: [13:04:26] Rep: 60 Mol:9 +141: [13:04:26] Rep: 60 Mol:13 +141: [13:04:26] Rep: 60 Mol:17 +141: [13:04:26] Rep: 60 Mol:21 +141: [13:04:26] Rep: 60 Mol:25 +141: [13:04:26] Rep: 60 Mol:29 +141: [13:04:26] Rep: 40 Mol:2 +141: [13:04:26] Rep: 40 Mol:6 +141: [13:04:26] Rep: 40 Mol:10 +141: [13:04:26] Rep: 40 Mol:14 +141: [13:04:26] Rep: 40 Mol:18 +141: [13:04:26] Rep: 40 Mol:22 +148: [13:04:26] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:26] Rep: 40 Mol:26 +141: [13:04:26] Rep: 40 Mol:30 +141: [13:04:26] Rep: 60 Mol:0 +141: [13:04:26] Rep: 60 Mol:4 +141: [13:04:26] Rep: 60 Mol:8 +141: [13:04:26] Rep: 60 Mol:12 +141: [13:04:26] Rep: 60 Mol:16 +141: [13:04:26] Rep: 60 Mol:20 +141: [13:04:26] Rep: 60 Mol:24 +141: [13:04:26] Rep: 80 Mol:3 +141: [13:04:26] Rep: 80 Mol:7 +141: [13:04:26] Rep: 80 Mol:11 +141: [13:04:26] Rep: 80 Mol:15 +141: [13:04:26] Rep: 80 Mol:19 +141: [13:04:26] Rep: 80 Mol:23 +141: [13:04:26] Rep: 80 Mol:27 +141: [13:04:26] Rep: 80 Mol:31 +148: [13:04:26] Molecule does not have explicit Hs. Consider calling AddHs() +141: [13:04:26] Rep: 60 Mol:28 +69: [13:04:26] Test multithreading (Done) +69: [13:04:26] ------------------------------------- +69: *************************************** +69: *************************************** +69: [13:04:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +69: [13:04:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +143/238 Test #108: pyFilterCatalog ........................ Passed 7.40 sec +test 185 + Start 185: pySubstructLibrary -181: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" -181: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap -181: Test timeout computed to be: 1500 -89: [03:35:40] Explicit valence for atom # 4 Al, 6, is greater than permitted -180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] -180: -180: 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, ] -180: -180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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, ] -180: -143: [03:35:40] Rep: 100 Mol:1 -143: [03:35:40] Rep: 100 Mol:5 -143: [03:35:40] Rep: 100 Mol:9 -143: [03:35:40] Rep: 100 Mol:13 -180: 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, ] -180: -180: 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, 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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] -180: -143: [03:35:40] Rep: 100 Mol:17 -143: [03:35:40] Rep: 100 Mol:21 -143: [03:35:40] Rep: 100 Mol:25 -143: [03:35:40] Rep: 100 Mol:29 -180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 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, 0.3, 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, 0.3, 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, ] -180: -180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 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, 0.3, 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, 0.3, 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, ] -180: -180: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] -180: -142/238 Test #180: testReducedGraphs ...................... Passed 0.12 sec -test 182 - Start 182: trajectoryTest +185: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" +185: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap +185: Test timeout computed to be: 1500 +69: [13:04:26] bond with order 0 found on line 7. This is not part of the MDL specification. +148: [13:04:26] Molecule does not have explicit Hs. Consider calling AddHs() +117: =>start test AUTOCORR3D custom +69: [13:04:26] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +69: [13:04:26] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +69: [13:04:26] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +117: [13:04:26] test on : 365 molecules done +69: generating smiles +69: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 +69: converting back +148: [13:04:26] Molecule does not have explicit Hs. Consider calling AddHs() +172: ..........[13:04:26] Too many matching bond pairs (1032) so can't continue. +69: check isomorphism +144/238 Test #182: trajectoryTest ......................... Passed 0.81 sec +test 186 + Start 186: testRGroupDecomp -182: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest -182: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory -182: Test timeout computed to be: 1500 -143/238 Test #108: pyFilterCatalog ........................ Passed 3.55 sec -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -89: [03:35:40] Explicit valence for atom # 10 Si, 6, is greater than permitted -test 183 - Start 183: substructLibraryTest +186: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp +186: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition +186: Test timeout computed to be: 1500 +148: [13:04:26] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[13:04:27] Molecule does not have explicit Hs. Consider calling AddHs() +143: [13:04:27] Rep: 100 Mol:2 +143: [13:04:27] Rep: 100 Mol:6 +143: [13:04:27] Rep: 100 Mol:10 +143: [13:04:27] Rep: 100 Mol:14 +126: Warning: Atom Count for residue LYS80A does not match expected count +143: [13:04:27] Rep: 100 Mol:18 +143: [13:04:27] Rep: 100 Mol:22 +143: [13:04:27] Rep: 100 Mol:26 +143: [13:04:27] Rep: 100 Mol:30 +183: [13:04:27] done +183: [13:04:27] ------------------------------------- +183: [13:04:27] Test2 +141: [13:04:27] Rep: 80 Mol:1 +141: [13:04:27] Rep: 80 Mol:5 +141: [13:04:27] Rep: 80 Mol:9 +141: [13:04:27] Rep: 80 Mol:13 +141: [13:04:27] Rep: 80 Mol:17 +141: [13:04:27] Rep: 80 Mol:21 +141: [13:04:27] Rep: 80 Mol:25 +141: [13:04:27] Rep: 80 Mol:29 +184: Randomness seeded to: 735471045 +184: =============================================================================== +184: All tests passed (171 assertions in 5 test cases) +184: +145/238 Test #184: substructLibraryCatchTest .............. Passed 0.94 sec +test 187 + Start 187: testRGroupDecompInternals -183: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest -183: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary -183: Test timeout computed to be: 1500 -141: [03:35:40] Rep: 20 Mol:2 -141: [03:35:40] Rep: 20 Mol:6 -141: [03:35:40] Rep: 20 Mol:10 -141: [03:35:40] Rep: 20 Mol:14 -141: [03:35:40] Rep: 20 Mol:18 -141: [03:35:40] Rep: 20 Mol:22 -141: [03:35:40] Rep: 20 Mol:26 -141: [03:35:40] Rep: 20 Mol:30 -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:35:40] Rep: 40 Mol:0 -141: [03:35:40] Rep: 40 Mol:4 -141: [03:35:40] Rep: 40 Mol:8 -141: [03:35:40] Rep: 40 Mol:12 -141: [03:35:40] Rep: 40 Mol:16 -141: [03:35:40] Rep: 40 Mol:20 -141: [03:35:40] Rep: 40 Mol:24 -141: [03:35:40] Rep: 40 Mol:28 -183: [03:35:40] ------------------------------------- -183: [03:35:40] Test1 -148: [03:35:40] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:41] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:41] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:41] Molecule does not have explicit Hs. Consider calling AddHs() -143: [03:35:41] Rep: 100 Mol:2 -143: [03:35:41] Rep: 100 Mol:6 -143: [03:35:41] Rep: 100 Mol:10 -143: [03:35:41] Rep: 100 Mol:14 -143: [03:35:41] Rep: 100 Mol:18 -143: [03:35:41] Rep: 100 Mol:22 -143: [03:35:41] Rep: 100 Mol:26 -148: [03:35:41] Molecule does not have explicit Hs. Consider calling AddHs() -143: [03:35:41] Rep: 100 Mol:30 -141: [03:35:41] Rep: 40 Mol:1 -141: [03:35:41] Rep: 40 Mol:5 -141: [03:35:41] Rep: 40 Mol:9 -141: [03:35:41] Rep: 40 Mol:13 -141: [03:35:41] Rep: 40 Mol:17 -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -141: [03:35:41] Rep: 40 Mol:21 -176: .... -176: ---------------------------------------------------------------------- -176: Ran 4 tests in 0.054s -176: -176: OK -148: [03:35:41] Molecule does not have explicit Hs. Consider calling AddHs() -141: [03:35:41] Rep: 40 Mol:25 -141: [03:35:41] Rep: 40 Mol:29 -141: [03:35:41] Rep: 60 Mol:3 -143: [03:35:41] Rep: 100 Mol:0 -143: [03:35:41] Rep: 100 Mol:4 -143: [03:35:41] Rep: 100 Mol:8 -143: [03:35:41] Rep: 100 Mol:12 -143: [03:35:41] Rep: 100 Mol:16 -143: [03:35:41] Rep: 100 Mol:20 -143: [03:35:41] Rep: 100 Mol:24 -143: [03:35:41] Rep: 100 Mol:28 -141: [03:35:41] Rep: 60 Mol:7 -141: [03:35:41] Rep: 60 Mol:11 -141: [03:35:41] Rep: 60 Mol:15 -141: [03:35:41] Rep: 60 Mol:19 -141: [03:35:41] Rep: 60 Mol:23 -141: [03:35:41] Rep: 60 Mol:27 -141: [03:35:41] Rep: 60 Mol:31 -148: [03:35:41] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:35:41] Molecule does not have explicit Hs. Consider calling AddHs() +187: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals +187: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition +187: Test timeout computed to be: 1500 +141: [13:04:27] Rep: 80 Mol:0 +141: [13:04:27] Rep: 80 Mol:4 +141: [13:04:27] Rep: 80 Mol:8 +141: [13:04:27] Rep: 80 Mol:12 +141: [13:04:27] Rep: 80 Mol:16 +141: [13:04:27] Rep: 80 Mol:20 +141: [13:04:27] Rep: 80 Mol:24 +141: [13:04:27] Rep: 80 Mol:28 +146: [13:04:23] --------------------------------- +146: [13:04:23] test3 +146: +146: [13:04:23] --------------------------------- +146: [13:04:23] test4 +146: +146: [13:04:23] --------------------------------- +146: [13:04:23] test5 +146: +146: [13:04:26] --------------------------------- +146: [13:04:26] test6 +146: +146: [13:04:26] --------------------------------- +146: [13:04:26] test15Dists +146: +146: [13:04:26] --------------------------------- +146: [13:04:26] test Issue 215 +146: +146: [13:04:26] --------------------------------- +146: [13:04:26] testMultipleConfs +146: +146: [13:04:26] --------------------------------- +146: [13:04:26] testMultipleConfsExpTors +146: +146: [13:04:27] --------------------------------- +146: [13:04:27] testIssue227 +146: +146: [13:04:27] --------------------------------- +146: [13:04:27] testIssue236 +146: +146: [13:04:27] --------------------------------- +146: [13:04:27] testOrdering +146: +146: [13:04:27] --------------------------------- +146: [13:04:27] testIssue244 +146: +146: [13:04:27] --------------------------------- +146: [13:04:27] testIssue251 +146: +146: [13:04:27] --------------------------------- +146: [13:04:27] testIssue276 +146: [13:04:27] --------------------------------- +146: [13:04:27] testIssue284 +146: +146: [13:04:27] --------------------------------- +146: [13:04:27] testIssue285 +146: +146: [13:04:27] --------------------------------- +146: [13:04:27] testIssue355 +146: +146: [13:04:27] --------------------------------- +146: [13:04:27] testRandomCoords +146: +146: [13:04:27] --------------------------------- +146: [13:04:27] test sf.net issue 1989539 +146: +146: [13:04:27] --------------------------------- +146: [13:04:27] test sf.net issue 2091864 +146: +146: [13:04:27] --------------------------------- +146: [13:04:27] test constrained embedding +146: +146: [13:04:27] ssd: 0.0752641 +146: [13:04:27] ssd: 0.0659363 +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +187: [13:04:27] WARNING: not removing hydrogen atom with dummy atom neighbors +146/238 Test #187: testRGroupDecompInternals .............. Passed 0.12 sec +test 188 + Start 188: rgroupCatchTests + +188: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests +188: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition +188: Test timeout computed to be: 1500 +141: [13:04:27] Rep: 60 Mol:2 +141: [13:04:27] Rep: 60 Mol:6 +141: [13:04:27] Rep: 60 Mol:10 +141: [13:04:27] Rep: 60 Mol:14 +141: [13:04:27] Rep: 60 Mol:18 +141: [13:04:27] Rep: 60 Mol:22 +141: [13:04:27] Rep: 60 Mol:26 +141: [13:04:27] Rep: 60 Mol:30 179: ..... 179: ---------------------------------------------------------------------- -179: Ran 5 tests in 0.042s +179: Ran 5 tests in 0.220s 179: 179: OK 179: Testing tert-butyldimethylsilyl @@ -29490,492 +29694,214 @@ 179: Testing acetamide 179: Testing carbobenzyloxy 179: Testing Acetal/Ketal -148: [03:35:41] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[03:35:41] Molecule does not have explicit Hs. Consider calling AddHs() -144/238 Test #179: pyDeprotect ............................ Passed 0.45 sec -test 184 - Start 184: substructLibraryCatchTest - -184: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest -184: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary -184: Test timeout computed to be: 1500 181: ..... 181: ---------------------------------------------------------------------- -181: Ran 5 tests in 0.021s +181: Ran 5 tests in 0.084s 181: 181: OK -29: All 191 tests passed -145/238 Test #176: pyCIPLabelsWrapTest .................... Passed 0.73 sec -test 185 - Start 185: pySubstructLibrary - -185: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" -185: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap -185: Test timeout computed to be: 1500 -89: [03:35:41] Explicit valence for atom # 2 O, 4, is greater than permitted -117: =>start test 1 WHIM custom -117: [03:35:41] test on : 365 molecules done -89: [03:35:41] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [03:35:41] Explicit valence for atom # 3 Be, 4, is greater than permitted -126: Warning: Atom Count for residue LYS80A does not match expected count -146/238 Test #181: pyReducedGraphs ........................ Passed 0.36 sec -test 186 - Start 186: testRGroupDecomp - -186: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp -186: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition -186: Test timeout computed to be: 1500 -89: [03:35:41] Explicit valence for atom # 27 P, 6, is greater than permitted -147/238 Test #182: trajectoryTest ......................... Passed 0.37 sec -test 187 - Start 187: testRGroupDecompInternals - -187: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals -187: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition -187: Test timeout computed to be: 1500 -141: [03:35:41] Rep: 40 Mol:2 -141: [03:35:41] Rep: 40 Mol:6 -141: [03:35:41] Rep: 40 Mol:10 -141: [03:35:41] Rep: 40 Mol:14 -147: [03:35:41] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -141: [03:35:41] Rep: 40 Mol:18 -141: [03:35:41] Rep: 40 Mol:22 -141: [03:35:41] Rep: 40 Mol:26 -141: [03:35:41] Rep: 40 Mol:30 -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -187: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors -148/238 Test #187: testRGroupDecompInternals .............. Passed 0.06 sec -test 188 - Start 188: rgroupCatchTests - -188: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests -188: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition -188: Test timeout computed to be: 1500 -89: =============================================================================== -89: All tests passed (21562 assertions in 3 test cases) -89: -149/238 Test #89: multithreadedSupplierCatchTest ......... Passed 4.07 sec -test 189 - Start 189: pyRGroupDecomposition - -189: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" -189: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap -189: Test timeout computed to be: 1500 -141: [03:35:41] Rep: 60 Mol:0 -141: [03:35:41] Rep: 60 Mol:4 -141: [03:35:41] Rep: 60 Mol:8 -141: [03:35:41] Rep: 60 Mol:12 -141: [03:35:41] Rep: 60 Mol:16 -141: [03:35:41] Rep: 60 Mol:20 -141: [03:35:41] Rep: 60 Mol:24 -141: [03:35:41] Rep: 60 Mol:28 -147: [03:35:41] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -141: [03:35:41] Rep: 60 Mol:1 -141: [03:35:41] Rep: 60 Mol:5 -141: [03:35:41] Rep: 60 Mol:9 -141: [03:35:41] Rep: 60 Mol:13 -141: [03:35:41] Rep: 60 Mol:17 -141: [03:35:41] Rep: 60 Mol:21 -141: [03:35:41] Rep: 60 Mol:25 -141: [03:35:41] Rep: 60 Mol:29 -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -141: [03:35:41] Rep: 80 Mol:3 -141: [03:35:41] Rep: 80 Mol:7 -141: [03:35:41] Rep: 80 Mol:11 -141: [03:35:41] Rep: 80 Mol:15 -141: [03:35:41] Rep: 80 Mol:19 -141: [03:35:41] Rep: 80 Mol:23 -141: [03:35:41] Rep: 80 Mol:27 -141: [03:35:41] Rep: 80 Mol:31 -147: [03:35:41] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -148: [03:35:41] Molecule does not have explicit Hs. Consider calling AddHs() -183: [03:35:41] done -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 4.358s -12: -12: OK -146: [03:35:39] --------------------------------- -146: [03:35:39] test3 -146: -146: [03:35:39] --------------------------------- -146: [03:35:39] test4 -146: -146: [03:35:39] --------------------------------- -146: [03:35:39] test5 -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] test6 -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] test15Dists -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] test Issue 215 -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] testMultipleConfs +147: [13:04:27] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: [13:04:27] Molecule does not have explicit Hs. Consider calling AddHs() +146: [13:04:27] --------------------------------- +146: [13:04:27] test sf.net issue 2091974 146: -146: [03:35:41] --------------------------------- -146: [03:35:41] testMultipleConfsExpTors +146: [13:04:27] --------------------------------- +146: [13:04:27] test sf.net issue 2835784 146: -146: [03:35:41] --------------------------------- -146: [03:35:41] testIssue227 +146: [13:04:27] --------------------------------- +146: [13:04:27] test sf.net issue 3019283 146: -146: [03:35:41] --------------------------------- -146: [03:35:41] testIssue236 +146: [13:04:27] --------------------------------- +146: [13:04:27] test sf.net issue 3238580 146: -146: [03:35:41] --------------------------------- -146: [03:35:41] testOrdering +146: [13:04:27] --------------------------------- +146: [13:04:27] test sf.net issue 3483968 146: -146: [03:35:41] --------------------------------- -146: [03:35:41] testIssue244 +146: [13:04:27] --------------------------------- +146: [13:04:27] test github issue 55 146: -146: [03:35:41] --------------------------------- -146: [03:35:41] testIssue251 +146: [13:04:27] --------------------------------- +146: [13:04:27] test1 146: -146: [03:35:41] --------------------------------- -146: [03:35:41] testIssue276 -146: [03:35:41] --------------------------------- -146: [03:35:41] testIssue284 +146: [13:04:27] --------------------------------- +146: [13:04:27] test multi-threading 146: -146: [03:35:41] --------------------------------- -146: [03:35:41] testIssue285 -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] testIssue355 -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] testRandomCoords -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] test sf.net issue 1989539 -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] test sf.net issue 2091864 -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] test constrained embedding -146: -146: [03:35:41] ssd: 0.0752641 -146: [03:35:41] ssd: 0.0659363 -183: [03:35:41] ------------------------------------- -183: [03:35:41] Test2 -150/238 Test #12: pyBV ................................... Passed 4.60 sec +146: building molecules +183: [13:04:27] done +125: Warning: Atom Count for residue GLU150A does not match expected count +183: [13:04:27] ------------------------------------- +183: [13:04:27] Test3 (stereo options) +146: generating reference data +147/238 Test #179: pyDeprotect ............................ Passed 1.72 sec +test 189 + Start 189: pyRGroupDecomposition + +189: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" +189: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap +189: Test timeout computed to be: 1500 +147: [13:04:27] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148/238 Test #181: pyReducedGraphs ........................ Passed 1.75 sec test 190 Start 190: determineBondsCatchTest 190: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DetermineBonds/determineBondsCatchTest 190: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DetermineBonds 190: Test timeout computed to be: 1500 -188: Randomness seeded to: 2361306650 -188: =============================================================================== -188: All tests passed (1475 assertions in 14 test cases) -188: -151/238 Test #188: rgroupCatchTests ....................... Passed 0.33 sec +125: Warning: Atom Count for residue ASN157A does not match expected count +117: =>start test 2 WHIM custom +117: [13:04:27] test on : 365 molecules done +183: [13:04:27] Done (stereo options) +183: [13:04:27] ------------------------------------- +183: [13:04:27] Test4 (trusted smiles) +147: [13:04:27] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +141: [13:04:27] Rep: 80 Mol:2 +141: [13:04:27] Rep: 80 Mol:6 +141: [13:04:27] Rep: 80 Mol:10 +141: [13:04:27] Rep: 80 Mol:14 +141: [13:04:27] Rep: 80 Mol:18 +141: [13:04:27] Rep: 80 Mol:22 +141: [13:04:27] Rep: 80 Mol:26 +141: [13:04:27] Rep: 80 Mol:30 +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +148: [13:04:28] Molecule does not have explicit Hs. Consider calling AddHs() +183: [13:04:28] Done (trusted smiles) +183: [13:04:28] ------------------------------------- +183: [13:04:28] Testing C++ docs +183: [13:04:28] Done (C++ doc tests) +183: [13:04:28] ------------------------------------- +183: [13:04:28] Testing C++ ring query: PatternHolder +183: [13:04:28] Done (C++ ring query tests) +183: [13:04:28] ------------------------------------- +183: [13:04:28] Testing C++ ring query: TautomerPatternHolder +183: [13:04:28] Done (C++ ring query tests) +183: [13:04:28] ------------------------------------- +183: [13:04:28] Add Patterns +147: [13:04:28] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: [13:04:28] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: [13:04:28] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +141: [13:04:28] done +141: [13:04:28] ------------------------------------- +141: [13:04:28] Test MMFF multithreading2 +186: [13:04:28] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +186: [13:04:28] WARNING: not removing hydrogen atom with dummy atom neighbors +29: All 191 tests passed +98: . +98: ---------------------------------------------------------------------- +98: Ran 11 tests in 6.169s +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 0.2018570899963379 seconds +98: Skipped 10000000 in 3.1171064376831055 seconds +98: Skipped 10000000 in 1.8272292613983154 seconds +148: [13:04:28] Molecule does not have explicit Hs. Consider calling AddHs() +151: 4733909071 +149/238 Test #98: pyChemReactionEnumerations ............. Passed 9.86 sec test 191 Start 191: pyDetermineBonds 191: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/DetermineBonds/Wrap/testDetermineBonds.py" 191: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/DetermineBonds/Wrap 191: Test timeout computed to be: 1500 -141: [03:35:41] Rep: 60 Mol:2 -141: [03:35:41] Rep: 60 Mol:6 -141: [03:35:41] Rep: 60 Mol:10 -141: [03:35:41] Rep: 60 Mol:14 -141: [03:35:41] Rep: 60 Mol:18 -141: [03:35:41] Rep: 60 Mol:22 -141: [03:35:41] Rep: 60 Mol:26 -141: [03:35:41] Rep: 60 Mol:30 -147: [03:35:41] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -125: Warning: Atom Count for residue GLU150A does not match expected count -141: [03:35:41] Rep: 80 Mol:1 -141: [03:35:41] Rep: 80 Mol:5 -141: [03:35:41] Rep: 80 Mol:9 -141: [03:35:41] Rep: 80 Mol:13 -141: [03:35:41] Rep: 80 Mol:17 -141: [03:35:41] Rep: 80 Mol:21 -141: [03:35:41] Rep: 80 Mol:25 -147: [03:35:41] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -141: [03:35:41] Rep: 80 Mol:29 -146: [03:35:41] --------------------------------- -146: [03:35:41] test sf.net issue 2091974 -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] test sf.net issue 2835784 -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] test sf.net issue 3019283 -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] test sf.net issue 3238580 -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] test sf.net issue 3483968 -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] test github issue 55 -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] test1 -146: -146: [03:35:41] --------------------------------- -146: [03:35:41] test multi-threading -146: -146: building molecules -141: [03:35:41] Rep: 80 Mol:0 -184: Randomness seeded to: 3555141128 -184: =============================================================================== -184: All tests passed (171 assertions in 5 test cases) -184: -141: [03:35:41] Rep: 80 Mol:4 -141: [03:35:41] Rep: 80 Mol:8 -152/238 Test #184: substructLibraryCatchTest .............. Passed 0.59 sec +141: [13:04:29] done +141: [13:04:29] ------------------------------------- +141: [13:04:29] Test MMFF multithreading3 +117: =>start test 1 WHIM custom +117: [13:04:29] test on : 365 molecules done +188: Randomness seeded to: 2096241342 +188: =============================================================================== +188: All tests passed (1475 assertions in 14 test cases) +188: +150/238 Test #188: rgroupCatchTests ....................... Passed 1.85 sec test 192 Start 192: molInterchangeTest1 192: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 192: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 192: Test timeout computed to be: 1500 -141: [03:35:41] Rep: 80 Mol:12 -141: [03:35:41] Rep: 80 Mol:16 -141: [03:35:41] Rep: 80 Mol:20 -141: [03:35:41] Rep: 80 Mol:24 -141: [03:35:41] Rep: 80 Mol:28 -146: generating reference data -147: [03:35:41] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -125: Warning: Atom Count for residue ASN157A does not match expected count -186: [03:35:41] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -192: [03:35:41] test1: basics -192: [03:35:41] done -192: [03:35:41] test2: basic writing +40: [13:04:29] done: 500000 +40: [13:04:29] Done +160: file testHandDrawn-5a.svg gave hash 3327818543U not the expected 1567781555U +160: [13:04:29] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [13:04:29] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +122: =>start test GETAWAY +122: [13:04:29] test on : 365 molecules done +143: [13:04:29] done +143: [13:04:29] ------------------------------------- +143: [13:04:29] Test UFF multithreading2 +148: [13:04:30] Molecule does not have explicit Hs. Consider calling AddHs() +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +151/238 Test #122: testGETAWAY ............................ Passed 11.81 sec +test 193 + Start 193: molInterchangeCatchTest + +193: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest +193: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange +193: Test timeout computed to be: 1500 +160: file testHandDrawn-5b.svg gave hash 2125846125U not the expected 66354106U +160: [13:04:31] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [13:04:31] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. +192: [13:04:31] test1: basics +192: [13:04:31] done +192: [13:04:31] test2: basic writing 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,0]}]}]} 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} -186: [03:35:41] WARNING: not removing hydrogen atom with dummy atom neighbors 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","aromaticAtoms":[0,1,2,3,4,5],"aromaticBonds":[0,1,2,3,4,5],"cipRanks":[0,0,0,0,0,0],"atomRings":[[0,5,4,3,2,1]]}]}]} 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","aromaticAtoms":[2,3,5,6,8,9],"aromaticBonds":[2,4,5,7,8,9],"cipRanks":[0,2,4,5,8,3,7,1,9,6],"atomRings":[[2,9,8,6,5,3]]}]}]} -192: [03:35:41] done -192: [03:35:41] test3: writing conformers +192: [13:04:31] done +192: [13:04:31] test3: writing conformers 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1988,-0.0452],[-0.3332,0.4556],[0.166,1.322],[0.5332,-0.0438],[-2.0652,0.4542],[-0.834,1.3212]]},{"dim":3,"coords":[[0.9554,-0.3743,-0.4679],[-0.3616,-0.1311,-0.0795],[-0.5097,1.6256,0.1706],[-0.5779,-0.792,1.1042],[1.5277,0.1064,0.1628],[-1.0339,-0.4346,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2025.03.1","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} -192: [03:35:41] done -192: [03:35:41] test4: writing properties +192: [13:04:31] done +192: [13:04:31] test4: writing properties 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"properties":{"foo_string":"bar","foo_int":1,"foo_double":1.2},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,0]}]}]} -192: [03:35:41] done -192: [03:35:41] test5: writing partial charges +192: [13:04:31] done +192: [13:04:31] test5: writing partial charges 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"z":8,"impHs":1}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2025.03.1","values":[0.5,-0.5]}]}]} -192: [03:35:41] testing parse options -192: [03:35:41] done -192: [03:35:41] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +192: [13:04:31] testing parse options +192: [13:04:31] done +192: [13:04:31] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 192: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":2},{"impHs":2},{"impHs":2},{"z":8},{"impHs":1,"stereo":"cw"},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2025.03.1","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -192: [03:35:41] done -192: [03:35:41] testing 'either' stereochemistry -192: [03:35:41] done -153/238 Test #192: molInterchangeTest1 .................... Passed 0.07 sec -test 193 - Start 193: molInterchangeCatchTest - -193: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest -193: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange -193: Test timeout computed to be: 1500 -69: [03:35:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:35:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:35:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:35:41] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -69: [03:35:41] deprecated group abbreviation ignored on line 24 -69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -69: [03:35:41] -69: -69: **** -69: Post-condition Violation -69: Element 'Mv' not found -69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -69: Failed Expression: anum > -1 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 3# 0x00007FD141CC8511 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 4# 0x00007FD141CD1DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 5# 0x00007FD141CD214D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 -69: 9# 0x0000563E0ECC3C15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 10# 0x0000563E0ED2A3F2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 11# 0x0000563E0ECAA9A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 12# 0x00007FD141233CA8 in /lib/x86_64-linux-gnu/libc.so.6 -69: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -69: 14# 0x0000563E0ECAAAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -193: Randomness seeded to: 2938460240 -193: [03:35:41] unrecognized bond type 12 set to zero while writing -193: [03:35:41] unrecognized bond type 0 set to zero while writing -193: =============================================================================== -193: All tests passed (125 assertions in 7 test cases) -193: -154/238 Test #193: molInterchangeCatchTest ................ Passed 0.08 sec +192: [13:04:31] done +192: [13:04:31] testing 'either' stereochemistry +192: [13:04:31] done +152/238 Test #192: molInterchangeTest1 .................... Passed 2.71 sec test 194 Start 194: pyMolInterchange 194: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 194: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 194: Test timeout computed to be: 1500 -40: [03:35:41] done: 500000 -40: [03:35:41] Done -148: [03:35:41] Molecule does not have explicit Hs. Consider calling AddHs() -111: [03:35:41] done -111: [03:35:41] ------------------------------------- -111: [03:35:41] Test Issue252: Bad definitions for Crippen atom types. -111: [03:35:41] done -111: [03:35:41] ------------------------------------- -111: [03:35:41] Test calculation of ChiVs. -183: [03:35:42] done -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test calculation of ChiNs. -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test calculation of HallKierAlpha. -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test calculation of Kappa1. -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test calculation of Kappa2. -183: [03:35:42] ------------------------------------- -183: [03:35:42] Test3 (stereo options) -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test calculation of Kappa3. -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test Crippen atom type calculations. -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test ring descriptors -69: [03:35:42] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -69: [03:35:42] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -141: [03:35:42] Rep: 80 Mol:2 -141: [03:35:42] Rep: 80 Mol:6 -141: [03:35:42] Rep: 80 Mol:10 -141: [03:35:42] Rep: 80 Mol:14 -141: [03:35:42] Rep: 80 Mol:18 -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test other count descriptors. -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test MQN -141: [03:35:42] Rep: 80 Mol:22 -111: [03:35:42] done -141: [03:35:42] Rep: 80 Mol:26 -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test GitHub Issue 56. -111: [03:35:42] WARNING: not removing hydrogen atom without neighbors -111: [03:35:42] WARNING: not removing hydrogen atom without neighbors -111: [03:35:42] WARNING: not removing hydrogen atom without neighbors -141: [03:35:42] Rep: 80 Mol:30 -111: [03:35:42] WARNING: not removing hydrogen atom without neighbors -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test Github92: Bad Crippen atom type for pyrrole H. -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test Github362: order dependence in Kier-Hall descriptors. -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test calculation of spiro and bridgehead counts. -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test Github694: ExactMolWt ignoring the mass of the electron -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Testing Properties and KitchenSink -111: [03:35:42] ---Caught keyerror (bad property name)--- -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test USR Descriptor -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test Github #1973: support P and S terms for TPSA calculation -111: [03:35:42] done -111: [03:35:42] ------------------------------------- -111: [03:35:42] Test Github #2948: Empty molecule has non-zero LabuteASA -111: [03:35:42] done -155/238 Test #111: testDescriptors ........................ Passed 4.68 sec +40: [13:04:31] Testing hanoi with a functor. +193: Randomness seeded to: 2056957660 +193: [13:04:31] unrecognized bond type 12 set to zero while writing +193: [13:04:31] unrecognized bond type 0 set to zero while writing +193: =============================================================================== +193: All tests passed (125 assertions in 7 test cases) +193: +153/238 Test #193: molInterchangeCatchTest ................ Passed 0.17 sec test 195 Start 195: testSLNParse 195: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 195: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse 195: Test timeout computed to be: 1500 -143: [03:35:42] done -143: [03:35:42] ------------------------------------- -143: [03:35:42] Test UFF multithreading2 -40: [03:35:42] Testing hanoi with a functor. -40: [03:35:42] Done -40: [03:35:42] Testing basic partition refinement. -69: ---------------------------------- -40: [03:35:42] Done -40: [03:35:42] Testing partition refinement with neighbors. -69: ---------------------------------- -40: [03:35:42] Done -40: [03:35:42] testing canonicalization via tie breaking. -40: [03:35:42] Done -40: [03:35:42] testing canonicalization using the wrapper. -69: [03:35:42] -69: -69: **** -69: Pre-condition Violation -69: rlabel out of range for MDL files -69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp -69: Failed Expression: rlabel >= 0 && rlabel < 100 -69: ---------- -69: Stacktrace: -69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -69: 3# 0x0000563E0ECD0FFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 4# 0x0000563E0ED2A46A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 5# 0x0000563E0ECAA9A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: 6# 0x00007FD141233CA8 in /lib/x86_64-linux-gnu/libc.so.6 -69: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -69: 8# 0x0000563E0ECAAAD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -69: ---------- -69: **** -69: -69: [03:35:42] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -40: [03:35:42] Done -40: [03:35:42] testing some specific ordering problems -40: [03:35:42] Finished -40: [03:35:42] testing chiral invariants. -40: [03:35:42] Finished -40: [03:35:42] testing unique ranks in w.r.t. renumbering. +40: [13:04:31] Done +40: [13:04:31] Testing basic partition refinement. +40: [13:04:31] Done +40: [13:04:31] Testing partition refinement with neighbors. +40: [13:04:31] Done +40: [13:04:31] testing canonicalization via tie breaking. +40: [13:04:31] Done +40: [13:04:31] testing canonicalization using the wrapper. 195: Atoms: 195: 0 6 C chg: 1 deg: 5 exp: N/A imp: 0 hyb: 195: 1 1 H chg: 0 deg: 1 exp: N/A imp: N/A hyb: @@ -29989,190 +29915,550 @@ 195: 2 0->3 order: 1 195: 3 0->4 order: 1 195: 4 0->5 order: 1 -195: [03:35:42] SLN Parse Error: syntax error while parsing: CH4[I=13] -195: [03:35:42] Failed parsing SLN 'CH4[I=13]' -195: [03:35:42] SLN Parser error: Atom ID 1 appears *after* its ring closure. -195: [03:35:42] SLN Parser error: Ring closure 1 does not have a corresponding opener. -195: [03:35:42] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -195: [03:35:42] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -195: [03:35:42] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -195: [03:35:42] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -195: [03:35:42] SLN Parse Error: syntax error while parsing: CH4 fff -195: [03:35:42] Failed parsing SLN 'CH4 fff' -195: [03:35:42] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -195: [03:35:42] Failed parsing SLN 'C[charge=+1] foo' -195: [03:35:42] Query property 'is' ignored on non-query atom -195: [03:35:42] Query property 'is' ignored on non-query atom -156/238 Test #195: testSLNParse ........................... Passed 0.08 sec +195: [13:04:32] SLN Parse Error: syntax error while parsing: CH4[I=13] +195: [13:04:32] Failed parsing SLN 'CH4[I=13]' +195: [13:04:32] SLN Parser error: Atom ID 1 appears *after* its ring closure. +195: [13:04:32] SLN Parser error: Ring closure 1 does not have a corresponding opener. +195: [13:04:32] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +195: [13:04:32] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +195: [13:04:32] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +195: [13:04:32] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +195: [13:04:32] SLN Parse Error: syntax error while parsing: CH4 fff +195: [13:04:32] Failed parsing SLN 'CH4 fff' +195: [13:04:32] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +195: [13:04:32] Failed parsing SLN 'C[charge=+1] foo' +40: [13:04:32] Done +40: [13:04:32] testing some specific ordering problems +40: [13:04:32] Finished +40: [13:04:32] testing chiral invariants. +40: [13:04:32] Finished +40: [13:04:32] testing unique ranks in w.r.t. renumbering. +195: [13:04:32] Query property 'is' ignored on non-query atom +195: [13:04:32] Query property 'is' ignored on non-query atom +154/238 Test #195: testSLNParse ........................... Passed 0.09 sec test 196 Start 196: pySLNParse 196: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/SLNParse/Wrap/testSLN.py" 196: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap 196: Test timeout computed to be: 1500 -183: [03:35:42] Done (stereo options) -183: [03:35:42] ------------------------------------- -183: [03:35:42] Test4 (trusted smiles) -40: [03:35:42] Finished -40: [03:35:42] testing mol fragments. -40: [03:35:42] Finished -40: [03:35:42] testing protein round-tripping. -148: [03:35:42] Molecule does not have explicit Hs. Consider calling AddHs() -194: .. -194: ---------------------------------------------------------------------- -194: Ran 2 tests in 0.025s -194: -194: OK -160: file testHandDrawn-5a.svg gave hash 3327818543U not the expected 1567781555U -160: [03:35:42] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:35:42] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -190: Randomness seeded to: 3902904616 -190: =============================================================================== -190: All tests passed (5174 assertions in 7 test cases) -190: -157/238 Test #190: determineBondsCatchTest ................ Passed 0.70 sec +126: Warning: Atom Count for residue GLU150A does not match expected count +141: [13:04:32] done +141: [13:04:32] ------------------------------------- +141: [13:04:32] Testing github 162: Incorrect SMILES after MMFF parameterization . +141: [13:04:32] done +141: [13:04:32] ------------------------------------- +141: [13:04:32] Testing github 224: crash during MMFF parameterization . +141: [13:04:32] done +141: [13:04:32] ------------------------------------- +141: [13:04:32] Testing github6728: crash due to missing stretch-bend params. +155/238 Test #141: testMMFFForceFieldHelpers .............. Passed 9.29 sec test 197 Start 197: pyGraphMolWrap 197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/rough_test.py" 197: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 197: Test timeout computed to be: 1500 -160: file testHandDrawn-5b.svg gave hash 2125846125U not the expected 66354106U -160: [03:35:42] Font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [03:35:42] Falling back to original font file /build/reproducible-path/rdkit-202503.1/Data/Fonts/Telex-Regular.ttf. -141: [03:35:42] done -141: [03:35:42] ------------------------------------- -141: [03:35:42] Test MMFF multithreading2 -158/238 Test #194: pyMolInterchange ....................... Passed 0.44 sec +160: file testHandDrawn-5.png gave hash 2441005674U not the expected 828378555U +126: Warning: Atom Count for residue ASN157A does not match expected count +160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U +143: [13:04:32] done +143: [13:04:32] ------------------------------------- +143: [13:04:32] Test UFF multithreading3 +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test Issue252: Bad definitions for Crippen atom types. +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test calculation of ChiVs. +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test calculation of ChiNs. +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test calculation of HallKierAlpha. +40: [13:04:32] Finished +40: [13:04:32] testing mol fragments. +40: [13:04:32] Finished +40: [13:04:32] testing protein round-tripping. +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test calculation of Kappa1. +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test calculation of Kappa2. +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test calculation of Kappa3. +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test Crippen atom type calculations. +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test ring descriptors +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test other count descriptors. +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test MQN +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test GitHub Issue 56. +111: [13:04:32] WARNING: not removing hydrogen atom without neighbors +111: [13:04:32] WARNING: not removing hydrogen atom without neighbors +111: [13:04:32] WARNING: not removing hydrogen atom without neighbors +111: [13:04:32] WARNING: not removing hydrogen atom without neighbors +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test Github92: Bad Crippen atom type for pyrrole H. +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test Github362: order dependence in Kier-Hall descriptors. +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test calculation of spiro and bridgehead counts. +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test Github694: ExactMolWt ignoring the mass of the electron +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Testing Properties and KitchenSink +148: [13:04:32] Molecule does not have explicit Hs. Consider calling AddHs() +111: [13:04:32] ---Caught keyerror (bad property name)--- +160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test USR Descriptor +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test Github #1973: support P and S terms for TPSA calculation +111: [13:04:32] done +111: [13:04:32] ------------------------------------- +111: [13:04:32] Test Github #2948: Empty molecule has non-zero LabuteASA +111: [13:04:32] done +156/238 Test #111: testDescriptors ........................ Passed 13.06 sec test 198 Start 198: pyTestConformerWrap 198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testConformer.py" 198: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 198: Test timeout computed to be: 1500 -191: .s.. -191: ---------------------------------------------------------------------- -191: Ran 4 tests in 0.397s -191: -191: OK (skipped=1) -183: [03:35:42] Done (trusted smiles) -183: [03:35:42] ------------------------------------- -183: [03:35:42] Testing C++ docs -183: [03:35:42] Done (C++ doc tests) -183: [03:35:42] ------------------------------------- -183: [03:35:42] Testing C++ ring query: PatternHolder -183: [03:35:42] Done (C++ ring query tests) -183: [03:35:42] ------------------------------------- -183: [03:35:42] Testing C++ ring query: TautomerPatternHolder -183: [03:35:42] Done (C++ ring query tests) -183: [03:35:42] ------------------------------------- -183: [03:35:42] Add Patterns -159/238 Test #191: pyDetermineBonds ....................... Passed 0.73 sec +172: .... +172: ---------------------------------------------------------------------- +172: Ran 14 tests in 6.382s +172: +172: OK +157/238 Test #172: pyRascalMCES ........................... Passed 7.84 sec test 199 Start 199: pyTestTrajectory 199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testTrajectory.py" 199: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 199: Test timeout computed to be: 1500 -143: [03:35:42] done -143: [03:35:42] ------------------------------------- -143: [03:35:42] Test UFF multithreading3 -172: .... -172: ---------------------------------------------------------------------- -172: Ran 14 tests in 1.916s -172: -172: OK -160: file testHandDrawn-5.png gave hash 2441005674U not the expected 828378555U 196: .. 196: ---------------------------------------------------------------------- -196: Ran 2 tests in 0.013s +196: Ran 2 tests in 0.036s 196: 196: OK -160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U -173: Randomness seeded to: 906656010 -173: [03:35:42] Writing the enumerated file may take quite some time and result in a large file. -151: 2711126092 -160/238 Test #196: pySLNParse ............................. Passed 0.42 sec +190: Randomness seeded to: 2903942131 +190: =============================================================================== +190: All tests passed (5174 assertions in 7 test cases) +190: +158/238 Test #190: determineBondsCatchTest ................ Passed 5.07 sec test 200 Start 200: pyTestSGroups 200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testSGroups.py" 200: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 200: Test timeout computed to be: 1500 -69: [03:35:42] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -69: [03:35:42] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -69: [03:35:42] Empty atom list: 'M ALS 1 0 F' on line 8. -161/238 Test #172: pyRascalMCES ........................... Passed 2.42 sec +143: [13:04:32] done +143: [13:04:32] ------------------------------------- +143: [13:04:32] Testing GitHubIssue62. +143: [13:04:32] beta-lactam 39.6387 +143: [13:04:32] cyclopropanone 174.698 +143: [13:04:32] aziridine 337.986 +143: [13:04:32] aziridinone 115.248 +143: [13:04:32] isobutene 2.48217 +143: [13:04:32] acetone 1.91788 +143: [13:04:32] cyclopentanone 10.1648 +143: [13:04:32] cyclopropene 99.4921 +143: [13:04:32] cyclobutene 41.0156 +143: [13:04:32] cyclopropane 267.236 +159/238 Test #196: pySLNParse ............................. Passed 0.92 sec test 201 Start 201: pyTestThreads 201: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testThreads.py" 201: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 201: Test timeout computed to be: 1500 -141: [03:35:42] done -141: [03:35:42] ------------------------------------- -141: [03:35:42] Test MMFF multithreading3 -162/238 Test #69: fileParsersTest1 ....................... Passed 5.51 sec -160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U +143: [13:04:32] gamma-lactam 15.7471 +146: validating reference data +143: [13:04:33] trans-2,3-diphenylcyclopropan-1-one 203.398 +69: [13:04:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [13:04:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [13:04:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +69: [13:04:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +198: ...... +198: ---------------------------------------------------------------------- +198: Ran 6 tests in 0.034s +198: +198: OK +160: [13:04:33] unrecognized bond typefile testGithub4238_1.png gave hash 2704600159U not the expected 2623427676U +69: [13:04:33] deprecated group abbreviation ignored on line 24 +69: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +69: [13:04:33] +69: +69: **** +69: Post-condition Violation +69: Element 'Mv' not found +69: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +69: Failed Expression: anum > -1 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 3# 0x00007FAA724C8511 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 4# 0x00007FAA724D1DCA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 5# 0x00007FAA724D214D in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitFileParsers.so.1 +69: 9# 0x00005654DCD6FC15 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 10# 0x00005654DCDD63F2 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 11# 0x00005654DCD569A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 12# 0x00007FAA71A33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +69: 13# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +69: 14# 0x00005654DCD56AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +160/238 Test #198: pyTestConformerWrap .................... Passed 0.74 sec test 202 Start 202: pyTestMultithreadedMolSupplier 202: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" 202: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 202: Test timeout computed to be: 1500 -126: Warning: Atom Count for residue GLU150A does not match expected count -143: [03:35:42] done -143: [03:35:42] ------------------------------------- -143: [03:35:42] Testing GitHubIssue62. -143: [03:35:42] beta-lactam 39.6387 -143: [03:35:42] cyclopropanone 174.698 -143: [03:35:42] aziridine 337.986 -143: [03:35:42] aziridinone 115.248 -143: [03:35:42] isobutene 2.48217 -143: [03:35:42] acetone 1.91788 -143: [03:35:42] cyclopentanone 10.1648 -143: [03:35:42] cyclopropene 99.4921 -143: [03:35:42] cyclobutene 41.0156 -143: [03:35:42] cyclopropane 267.236 -143: [03:35:42] gamma-lactam 15.7471 -143: [03:35:42] trans-2,3-diphenylcyclopropan-1-one 203.398 -126: Warning: Atom Count for residue ASN157A does not match expected count -143: [03:35:42] cis-2,3-diphenylcyclopropan-1-one 206.852 -160: [03:35:42] unrecognized bond typefile testGithub4238_1.png gave hash 2704600159U not the expected 2623427676U +143: [13:04:33] cis-2,3-diphenylcyclopropan-1-one 206.852 +160: file testGithub4323_1.png gave hash 1936109620U not the expected 3075787867U +151: 4165159625 +151: =============================================================================== +151: All tests passed (73 assertions in 3 test cases) +151: +194: .. +194: ---------------------------------------------------------------------- +194: Ran 2 tests in 0.069s +194: +194: OK +143: [13:04:33] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +173: Randomness seeded to: 149385856 +173: [13:04:33] Writing the enumerated file may take quite some time and result in a large file. +161/238 Test #151: molAlignCatchTest ...................... Passed 9.56 sec +test 203 + Start 203: pyTestPropertyLists + +203: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testPropertyLists.py" +203: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +203: Test timeout computed to be: 1500 +143: [13:04:33] cyclopropylidencyclobutane 218.879 +197: ..............[13:04:33] SMARTS Parse Error: syntax error while parsing: fiib +197: [13:04:33] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +143: [13:04:33] diphenylmethylidencyclobutane 79.6139 +143: [13:04:33] done +143: [13:04:33] ------------------------------------- +143: [13:04:33] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +143: [13:04:33] done +143: [13:04:33] ------------------------------------- +143: [13:04:33] Test square planar complexes +143: [13:04:33] done +143: [13:04:33] ------------------------------------- +143: [13:04:33] Test octahedral complexes +143: [13:04:33] done +162/238 Test #143: testUFFForceFieldHelpers ............... Passed 10.51 sec +test 204 + Start 204: pyCDXMLTest + +204: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/test_cdxml.py" +204: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +204: Test timeout computed to be: 1500 +197: ....[13:04:33] ERROR: Problems encountered parsing data fields +197: [13:04:33] ERROR: moving to the beginning of the next molecule +197: [13:04:33] ERROR: Problems encountered parsing data fields +197: [13:04:33] ERROR: moving to the beginning of the next molecule +197: [13:04:33] Spurious data before the first property will be ignored +197: [13:04:33] Property will be truncated after the first blank line +197: [13:04:33] Property will be truncated after the first blank line +197: [13:04:33] Property will be truncated after the first blank line +197: [13:04:33] ERROR: Problems encountered parsing data fields +197: [13:04:33] ERROR: moving to the beginning of the next molecule +197: [13:04:33] ERROR: Problems encountered parsing data fields +197: [13:04:33] ERROR: moving to the beginning of the next molecule +197: [13:04:33] Spurious data before the first property will be ignored +197: [13:04:33] Property will be truncated after the first blank line +197: [13:04:33] Property will be truncated after the first blank line +197: [13:04:33] Property will be truncated after the first blank line +197: [13:04:33] ERROR: Problems encountered parsing data fields +197: [13:04:33] ERROR: moving to the beginning of the next molecule +197: [13:04:33] Property will be truncated after the first blank line +197: [13:04:33] ERROR: Problems encountered parsing data fields +197: [13:04:33] ERROR: moving to the beginning of the next molecule +197: [13:04:33] Property will be truncated after the first blank line +197: .[13:04:33] SMILES Parse Error: syntax error while parsing: fail +197: [13:04:33] SMILES Parse Error: check for mistakes around position 1: +197: [13:04:33] fail +197: [13:04:33] ^ +197: [13:04:33] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +197: [13:04:33] ERROR: Smiles parse error on line 2 +197: [13:04:33] ERROR: Cannot create molecule from : 'fail' +197: >>> This may result in an infinite loop. It should finish almost instantly +197: <<< OK, it finished. +197: ............[13:04:33] Explicit valence for atom # 1 C, 5, is greater than permitted +197: ......[13:04:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197: [13:04:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197: [13:04:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197: [13:04:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +197: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| +163/238 Test #194: pyMolInterchange ....................... Passed 1.70 sec +test 205 + Start 205: molStandardizeTest + +205: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest +205: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +205: Test timeout computed to be: 1500 +197: ........[13:04:33] non-ring atom 0 marked aromatic +197: [13:04:33] non-ring atom 0 marked aromatic +197: [13:04:33] +197: +197: **** +200: ............. +200: ---------------------------------------------------------------------- +200: Ran 13 tests in 0.051s +200: +200: OK +200: Testing SubstanceGroups wrapper +197: Range Error +197: idx +197: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +197: Failed Expression: 12 < 6 +197: ---------- +197: Stacktrace: +197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +197: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +197: 4# 0x00007F3EF0E84A30 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x00007F3EF36E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +197: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so +197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x00007F3EF0DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x00007F3EF0DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x00007F3EF0DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x00007F3EF0DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 21# 0x00007F3EF0DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 27# 0x00007F3EF36E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 28# _PyObject_MakeTpCall in /usr/bin/python3 +197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 30# 0x00000000005CBA19 in /usr/bin/python3 +197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 32# 0x000000000068AE3F in /usr/bin/python3 +197: 33# 0x000000000062A0B0 in /usr/bin/python3 +197: 34# _PyObject_MakeTpCall in /usr/bin/python3 +197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 36# 0x00000000005CBA19 in /usr/bin/python3 +197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 38# 0x000000000068AE3F in /usr/bin/python3 +197: 39# 0x000000000062A0B0 in /usr/bin/python3 +197: 40# _PyObject_MakeTpCall in /usr/bin/python3 +197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 42# 0x00000000005CBA19 in /usr/bin/python3 +197: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 44# 0x000000000068AE3F in /usr/bin/python3 +197: 45# 0x000000000062A0B0 in /usr/bin/python3 +197: 46# _PyObject_MakeTpCall in /usr/bin/python3 +197: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 48# 0x000000000059F272 in /usr/bin/python3 +197: 49# _PyObject_MakeTpCall in /usr/bin/python3 +197: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 51# PyEval_EvalCode in /usr/bin/python3 +197: 52# 0x00000000006A5B71 in /usr/bin/python3 +197: 53# 0x00000000006A2C1E in /usr/bin/python3 +197: 54# 0x00000000006B3B53 in /usr/bin/python3 +197: 55# 0x00000000006B3563 in /usr/bin/python3 +197: 56# 0x00000000006B339E in /usr/bin/python3 +197: 57# Py_RunMain in /usr/bin/python3 +197: 58# Py_BytesMain in /usr/bin/python3 +197: 59# 0x00007F3EF3ECFCA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +197: 61# _start in /usr/bin/python3 +197: ---------- +197: **** +197: +197: [13:04:33] non-ring atom 0 marked aromatic +197: [13:04:33] non-ring atom 0 marked aromatic +197: [13:04:33] +197: +197: **** +197: Range Error +197: idx +197: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp +197: Failed Expression: 12 < 6 +197: ---------- +197: Stacktrace: +197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +197: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +197: 4# 0x00007F3EF0E84A30 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x00007F3EF36E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so +197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so +197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +197: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so +197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so +197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x00007F3EF0DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x00007F3EF0DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x00007F3EF0DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x00007F3EF0DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 21# 0x00007F3EF0DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so +197: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 27# 0x00007F3EF36E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 28# _PyObject_MakeTpCall in /usr/bin/python3 +197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 30# 0x00000000005CBA19 in /usr/bin/python3 +197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 32# 0x000000000068AE3F in /usr/bin/python3 +197: 33# 0x000000000062A0B0 in /usr/bin/python3 +197: 34# _PyObject_MakeTpCall in /usr/bin/python3 +197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 36# 0x00000000005CBA19 in /usr/bin/python3 +197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 38# 0x000000000068AE3F in /usr/bin/python3 +197: 39# 0x000000000062A0B0 in /usr/bin/python3 +197: 40# _PyObject_MakeTpCall in /usr/bin/python3 +197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 42# 0x00000000005CBA19 in /usr/bin/python3 +197: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 44# 0x000000000068AE3F in /usr/bin/python3 +197: 45# 0x000000000062A0B0 in /usr/bin/python3 +197: 46# _PyObject_MakeTpCall in /usr/bin/python3 +197: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 48# 0x000000000059F272 in /usr/bin/python3 +197: 49# _PyObject_MakeTpCall in /usr/bin/python3 +197: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +197: 51# PyEval_EvalCode in /usr/bin/python3 +197: 52# 0x00000000006A5B71 in /usr/bin/python3 +197: 53# 0x00000000006A2C1E in /usr/bin/python3 +197: 54# 0x00000000006B3B53 in /usr/bin/python3 +197: 55# 0x00000000006B3563 in /usr/bin/python3 +197: 56# 0x00000000006B339E in /usr/bin/python3 +197: 57# Py_RunMain in /usr/bin/python3 +197: 58# Py_BytesMain in /usr/bin/python3 +197: 59# 0x00007F3EF3ECFCA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +197: 61# _start in /usr/bin/python3 +197: ---------- +197: **** +197: +148: [13:04:33] Molecule does not have explicit Hs. Consider calling AddHs() +191: .s.. +191: ---------------------------------------------------------------------- +191: Ran 4 tests in 0.893s +191: +191: OK (skipped=1) +203: [13:04:33] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +203: [13:04:33] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +203: [13:04:33] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +203: .[13:04:33] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +203: [13:04:33] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +203: [13:04:33] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +203: ...[13:04:33] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +203: [13:04:33] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +203: [13:04:33] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +203: . +203: ---------------------------------------------------------------------- +203: Ran 5 tests in 0.015s +203: +203: OK +197: ...............[13:04:33] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +197: [13:04:33] 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. +164/238 Test #203: pyTestPropertyLists .................... Passed 0.52 sec +test 206 + Start 206: molNormalizeTest + +206: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest +206: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +206: Test timeout computed to be: 1500 +69: [13:04:33] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +69: [13:04:33] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +165/238 Test #191: pyDetermineBonds ....................... Passed 4.82 sec +test 207 + Start 207: molValidateTest + +207: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest +207: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +207: 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 0.104 seconds +163: Time elapsed 0.254 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 0.010 seconds +163: Time elapsed 0.043 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 0.015 seconds +163: Time elapsed 0.063 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 0.132 seconds +163: Time elapsed 0.420 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 0.183 seconds +163: Time elapsed 0.334 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 0.222 seconds +163: Time elapsed 0.403 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 0.201 seconds +163: Time elapsed 0.400 seconds 163: 163: testSegFault() 163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.012 seconds +163: Time elapsed 0.034 seconds 163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.020 seconds +163: Time elapsed 0.055 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 0.014 seconds +163: Time elapsed 0.055 seconds 163: 163: testThreshold() 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds @@ -30180,11 +30466,11 @@ 163: 163: testRing1() 163: MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds -163: Time elapsed 0.560 seconds +163: Time elapsed 1.479 seconds 163: MCS MatchFusedRings: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds -163: Time elapsed 0.573 seconds +163: Time elapsed 4.119 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 0.728 seconds +163: Time elapsed 1.733 seconds 163: 163: testAtomCompareIsotopes() 163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds @@ -30208,16 +30494,11 @@ 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 0.013 seconds -163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds -198: ...... -198: ---------------------------------------------------------------------- -198: Ran 6 tests in 0.048s -198: -198: OK -199: [03:35:42] +199: [13:04:33] 199: 199: **** +163: Time elapsed 0.037 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 199: Pre-condition Violation 199: from must be < size() 199: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30229,23 +30510,23 @@ 199: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x00007FADFC76362C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x00007F8833F1262C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x00007FADFA3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x00007FADFA3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x00007FADFA3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x00007FADFA3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x00007FADFA3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x00007F88319B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x00007F88319B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x00007F88319B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x00007F88319B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x00007F88319B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x00007FADFC7603C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x00007F8833F0F3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x00000000005CBA19 in /usr/bin/python3 @@ -30277,16 +30558,22 @@ 199: 50# 0x00000000006B339E in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x00007FADFCF0DCA8 in /lib/x86_64-linux-gnu/libc.so.6 +199: 53# 0x00007F88346BCCA8 in /lib/x86_64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -143: [03:35:42] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -199: .[03:35:42] +199: .[13:04:33] 199: 199: **** +166/238 Test #200: pyTestSGroups .......................... Passed 0.99 sec +test 208 + Start 208: molChargeTest + +208: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest +208: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +208: Test timeout computed to be: 1500 199: Pre-condition Violation 199: from must be < size() 199: Violation occurred on line 91 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30298,23 +30585,23 @@ 199: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x00007FADFC76362C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x00007F8833F1262C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x00007FADFA3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x00007FADFA3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x00007FADFA3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x00007FADFA3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x00007FADFA3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x00007F88319B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x00007F88319B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x00007F88319B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x00007F88319B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x00007F88319B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x00007FADFC7603C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x00007F8833F0F3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x00000000005CBA19 in /usr/bin/python3 @@ -30346,77 +30633,170 @@ 199: 50# 0x00000000006B339E in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x00007FADFCF0DCA8 in /lib/x86_64-linux-gnu/libc.so.6 +199: 53# 0x00007F88346BCCA8 in /lib/x86_64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -160: file testGithub4323_1.png gave hash 1936109620U not the expected 3075787867U -143: [03:35:42] cyclopropylidencyclobutane 218.879 -148: [03:35:42] Molecule does not have explicit Hs. Consider calling AddHs() -163/238 Test #198: pyTestConformerWrap .................... Passed 0.63 sec -test 203 - Start 203: pyTestPropertyLists +206: [13:04:33] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +207: ERROR: [FeaturesValidation] Query atom 0 is not allowed +207: ERROR: [FeaturesValidation] Dummy atom 0 is not allowed +207: ERROR: [FeaturesValidation] Query bond 0 is not allowed +207: ERROR: [FeaturesValidation] Bond 0 of aromatic type is not allowed +207: ERROR: [FeaturesValidation] Bond 1 of aromatic type is not allowed +207: ERROR: [FeaturesValidation] Bond 2 of aromatic type is not allowed +207: ERROR: [FeaturesValidation] Bond 3 of aromatic type is not allowed +207: ERROR: [FeaturesValidation] Bond 5 of aromatic type is not allowed +207: ERROR: [FeaturesValidation] Bond 6 of aromatic type is not allowed +207: ERROR: [FeaturesValidation] Bond 2 of dative type is not allowed +207: ERROR: [FeaturesValidation] Bond 3 of dative type is not allowed +207: ERROR: [FeaturesValidation] Atom 2 with alias 'CF3' is not allowed +207: ERROR: [FeaturesValidation] Enhanced stereochemistry features are not allowed +207: ERROR: [StereoValidation] Atom 3 has both unknown and wedged/dashed stereo bonds. +207: here +207: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. +207: there +207: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. +167/238 Test #207: molValidateTest ........................ Passed 0.17 sec +test 209 + Start 209: molTautomerTest -203: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/testPropertyLists.py" -203: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -203: Test timeout computed to be: 1500 -141: [03:35:42] done -141: [03:35:42] ------------------------------------- -141: [03:35:42] Testing github 162: Incorrect SMILES after MMFF parameterization . -141: [03:35:42] done -141: [03:35:42] ------------------------------------- -141: [03:35:42] Testing github 224: crash during MMFF parameterization . -141: [03:35:42] done -141: [03:35:42] ------------------------------------- -141: [03:35:42] Testing github6728: crash due to missing stretch-bend params. -143: [03:35:43] diphenylmethylidencyclobutane 79.6139 -143: [03:35:43] done -143: [03:35:43] ------------------------------------- -143: [03:35:43] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -143: [03:35:43] done -143: [03:35:43] ------------------------------------- -143: [03:35:43] Test square planar complexes -143: [03:35:43] done -143: [03:35:43] ------------------------------------- -143: [03:35:43] Test octahedral complexes -164/238 Test #141: testMMFFForceFieldHelpers .............. Passed 3.44 sec -143: [03:35:43] done -test 204 - Start 204: pyCDXMLTest +209: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest +209: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +209: Test timeout computed to be: 1500 +189: .................... +189: ---------------------------------------------------------------------- +189: Ran 20 tests in 5.595s +189: +189: OK +197: ..............[13:04:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +197: [13:04:33] Explicit valence for atom # 1 C, 5, is greater than permitted +206: [13:04:34] Initializing Normalizer +206: [13:04:34] Running Normalizer +206: [13:04:34] Rule applied: BrokenazidetoN=N+=N- +206: [13:04:34] Initializing Normalizer +206: [13:04:34] Running Normalizer +206: [13:04:34] Initializing Normalizer +206: [13:04:34] Running Normalizer +168/238 Test #206: molNormalizeTest ....................... Passed 0.28 sec +test 210 + Start 210: molStandardizeSmallTest -204: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Wrap/test_cdxml.py" -204: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -204: Test timeout computed to be: 1500 -165/238 Test #143: testUFFForceFieldHelpers ............... Passed 3.44 sec -test 205 - Start 205: molStandardizeTest +210: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest +210: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +210: Test timeout computed to be: 1500 +148: [13:04:34] Molecule does not have explicit Hs. Consider calling AddHs() +69: ---------------------------------- +69: ---------------------------------- +69: [13:04:34] +69: +69: **** +69: Pre-condition Violation +69: rlabel out of range for MDL files +69: Violation occurred on line 863 in file ./Code/GraphMol/Atom.cpp +69: Failed Expression: rlabel >= 0 && rlabel < 100 +69: ---------- +69: Stacktrace: +69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 +69: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +69: 3# 0x00005654DCD7CFFF in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 4# 0x00005654DCDD646A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 5# 0x00005654DCD569A3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: 6# 0x00007FAA71A33CA8 in /lib/x86_64-linux-gnu/libc.so.6 +69: 7# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 +69: 8# 0x00005654DCD56AD1 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +69: ---------- +69: **** +69: +69: [13:04:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +169/238 Test #208: molChargeTest .......................... Passed 0.38 sec +test 211 + Start 211: molFragmentTest -205: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest -205: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -205: Test timeout computed to be: 1500 -40: [03:35:43] Finished -40: [03:35:43] testing stability w.r.t. renumbering. -163: Time elapsed 0.002 seconds +211: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest +211: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +211: Test timeout computed to be: 1500 +160: file testGithub4323_3.png gave hash 1732257634U not the expected 381907253U +170/238 Test #210: molStandardizeSmallTest ................ Passed 0.19 sec +test 212 + Start 212: molStandardizeCatchTest + +212: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest +212: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +212: Test timeout computed to be: 1500 +160: [13:04:34] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +171/238 Test #189: pyRGroupDecomposition .................. Passed 6.60 sec +test 213 + Start 213: molStandardizePipelineTest + +213: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest +213: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +213: Test timeout computed to be: 1500 +213: Randomness seeded to: 2535121423 +202: .s. +202: ---------------------------------------------------------------------- +202: Ran 3 tests in 0.311s +202: +202: OK (skipped=1) +202: Testing Smiles and SD MultithreadedMolSupplier +213: 1 Counts line too short: '' on line4 +213: 1 Could not instantiate a valid molecule from input +211: [13:04:34] SMARTS Parse Error: syntax error while parsing: [Cl +211: [13:04:34] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +213: 8 Molecule has no atoms +213: [13:04:34] Explicit valence for atom # 1 N, 4, is greater than permitted +213: [13:04:34] Explicit valence for atom # 1 N, 4, is greater than permitted +172/238 Test #211: molFragmentTest ........................ Passed 0.16 sec +test 214 + Start 214: pyMolStandardize + +214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" +214: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap +214: Test timeout computed to be: 1500 +213: 8 Explicit valence for atom # 1 N, 4, is greater than permitted +213: 128 An error occurred while preparing the molecule for standardization. +213: 8 The molecule contains an unknown isotope: 3C +213: 4 Query atom 0 is not allowed +213: 4 Bond 0 of aromatic type is not allowed +213: 4 Bond 1 of aromatic type is not allowed +213: 4 Bond 2 of aromatic type is not allowed +213: 4 Bond 3 of aromatic type is not allowed +213: 4 Bond 5 of aromatic type is not allowed +213: 4 Bond 6 of aromatic type is not allowed +213: 4 Bond 2 of dative type is not allowed +213: 4 Bond 3 of dative type is not allowed +213: 4 Enhanced stereochemistry features are not allowed +213: 8 The radical at atom 0 is not allowed +213: [13:04:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +213: 16 The molecule includes non-null Z coordinates +213: 32 Atom 0 too close to bond 2 +213: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit +213: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds +213: 64 Atom 0 has adjacent stereo bonds with like orientation +213: [13:04:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +213: 16 The molecule includes non-null Z coordinates +213: 64 Atom 0 has adjacent stereo bonds with like orientation +163: Time elapsed 0.010 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 0.007 seconds +163: Time elapsed 0.035 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 0.102 seconds +163: Time elapsed 0.455 seconds 163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -163: Time elapsed 0.001 seconds +163: Time elapsed 0.017 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 0.030 seconds +163: Time elapsed 0.125 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 0.0011 seconds. bond[0]=6 +163: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0215 seconds. bond[0]=6 163: STATISTICS: -163: Total Growing Steps = 1, MCS found on 1 step, for 0.0011 seconds +163: Total Growing Steps = 1, MCS found on 1 step, for 0.0215 seconds 163: Initial Seeds = 1, Mismatched 0 163: Inspected Seeds = 2 163: Rejected by BestSize = 0 @@ -30435,7 +30815,7 @@ 163: HashFoundInCache= 0 163: ExactMatchCalls = 0 163: ExactMatchFound = 0 -163: Time elapsed 0.001 seconds +163: Time elapsed 0.022 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 @@ -30509,6 +30889,12 @@ 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 +213: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit +213: 8388608 One or more metal atoms were disconnected. +213: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +213: 67108864 The protonation state was adjusted. +213: 16777216 The representation of some functional groups was adjusted. +213: 67108864 The protonation state was adjusted. 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 @@ -30531,26 +30917,55 @@ 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: done -200: ............. -200: ---------------------------------------------------------------------- -200: Ran 13 tests in 0.024s -200: -200: OK -200: Testing SubstanceGroups wrapper -40: [03:35:43] Finished -40: [03:35:43] testing smiles round-tripping. -166/238 Test #200: pyTestSGroups .......................... Passed 0.56 sec -test 206 - Start 206: molNormalizeTest +213: 16777216 The representation of some functional groups was adjusted. +213: 67108864 The protonation state was adjusted. +213: 16777216 The representation of some functional groups was adjusted. +173/238 Test #202: pyTestMultithreadedMolSupplier ......... Passed 1.38 sec +test 215 + Start 215: testScaffoldNetwork -206: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest -206: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -206: Test timeout computed to be: 1500 -197: ..............[03:35:43] SMARTS Parse Error: syntax error while parsing: fiib -197: [03:35:43] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -199: .[03:35:43] +215: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork +215: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork +215: Test timeout computed to be: 1500 +213: 16777216 The representation of some functional groups was adjusted. +213: 67108864 The protonation state was adjusted. +213: 16777216 The representation of some functional groups was adjusted. +213: 67108864 The protonation state was adjusted. +213: 16777216 The representation of some functional groups was adjusted. +213: 67108864 The protonation state was adjusted. +213: 16777216 The representation of some functional groups was adjusted. +213: 67108864 The protonation state was adjusted. +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 15.819s +12: +12: OK +213: 8388608 One or more metal atoms were disconnected. +213: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +148: [13:04:34] Molecule does not have explicit Hs. Consider calling AddHs() +204: . +204: ---------------------------------------------------------------------- +204: Ran 1 test in 0.062s +204: +204: OK +213: 67108864 The protonation state was adjusted. +213: 8388608 One or more metal atoms were disconnected. +213: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +213: 67108864 The protonation state was adjusted. +40: [13:04:34] Finished +40: [13:04:34] testing stability w.r.t. renumbering. +213: 8388608 One or more metal atoms were disconnected. +213: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +213: 67108864 The protonation state was adjusted. +213: 8388608 One or more metal atoms were disconnected. +213: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +213: 67108864 The protonation state was adjusted. +199: .[13:04:34] 199: 199: **** +213: 8388608 One or more metal atoms were disconnected. +213: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +213: 67108864 The protonation state was adjusted. 199: Range Error 199: snapshotNum 199: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30563,23 +30978,23 @@ 199: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 6# 0x00007FADFC76362C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 6# 0x00007F8833F1262C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x00007FADFA3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x00007FADFA3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x00007FADFA3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x00007FADFA3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 16# 0x00007FADFA3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x00007F88319B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x00007F88319B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x00007F88319B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x00007F88319B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 16# 0x00007F88319B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 22# 0x00007FADFC7603C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 22# 0x00007F8833F0F3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 23# _PyObject_MakeTpCall in /usr/bin/python3 199: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 25# 0x00000000005CBA19 in /usr/bin/python3 @@ -30611,13 +31026,13 @@ 199: 51# 0x00000000006B339E in /usr/bin/python3 199: 52# Py_RunMain in /usr/bin/python3 199: 53# Py_BytesMain in /usr/bin/python3 -199: 54# 0x00007FADFCF0DCA8 in /lib/x86_64-linux-gnu/libc.so.6 +199: 54# 0x00007F88346BCCA8 in /lib/x86_64-linux-gnu/libc.so.6 199: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 199: 56# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: .[03:35:43] +199: .[13:04:34] 199: 199: **** 199: Pre-condition Violation @@ -30631,23 +31046,23 @@ 199: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x00007FADFC76362C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x00007F8833F1262C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x00007FADFA3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x00007FADFA3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x00007FADFA3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x00007FADFA3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x00007FADFA3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x00007F88319B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x00007F88319B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x00007F88319B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x00007F88319B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x00007F88319B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x00007FADFC7603C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x00007F8833F0F3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x00000000005CBA19 in /usr/bin/python3 @@ -30679,13 +31094,14 @@ 199: 50# 0x00000000006B339E in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x00007FADFCF0DCA8 in /lib/x86_64-linux-gnu/libc.so.6 +199: 53# 0x00007F88346BCCA8 in /lib/x86_64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: ..[03:35:43] +213: 16777216 The "wavy" style of bond 4 was removed +199: ..[13:04:34] 199: 199: **** 199: Pre-condition Violation @@ -30699,23 +31115,23 @@ 199: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x00007FADFC76362C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x00007F8833F1262C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x00007FADFA3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x00007FADFA3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x00007FADFA3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x00007FADFA3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x00007FADFA3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x00007F88319B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x00007F88319B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x00007F88319B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x00007F88319B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x00007F88319B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x00007FADFC7603C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x00007F8833F0F3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x00000000005CBA19 in /usr/bin/python3 @@ -30747,13 +31163,13 @@ 199: 50# 0x00000000006B339E in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x00007FADFCF0DCA8 in /lib/x86_64-linux-gnu/libc.so.6 +199: 53# 0x00007F88346BCCA8 in /lib/x86_64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: .[03:35:43] +199: .[13:04:34] 199: 199: **** 199: Pre-condition Violation @@ -30767,23 +31183,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x00007FADFC76362C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x00007F8833F1262C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x00007FADFA3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x00007FADFA3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x00007FADFA3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x00007FADFA3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x00007FADFA3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x00007F88319B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x00007F88319B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x00007F88319B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x00007F88319B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x00007F88319B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x00007FADFC7603C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x00007F8833F0F3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x00000000005CBA19 in /usr/bin/python3 @@ -30815,15 +31231,17 @@ 199: 50# 0x00000000006B339E in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x00007FADFCF0DCA8 in /lib/x86_64-linux-gnu/libc.so.6 +199: 53# 0x00007F88346BCCA8 in /lib/x86_64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: [03:35:43] +199: [13:04:34] 199: 199: **** +213: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration +213: 16777216 The "wavy" style of bond 2 was removed 199: Pre-condition Violation 199: d_trajectory must not be NULL 199: Violation occurred on line 24 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30835,23 +31253,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x00007FADFC76362C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x00007F8833F1262C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x00007FADFA3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x00007FADFA3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x00007FADFA3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x00007FADFA3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x00007FADFA3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x00007F88319B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x00007F88319B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x00007F88319B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x00007F88319B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x00007F88319B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x00007FADFC7603C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x00007F8833F0F3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x00000000005CBA19 in /usr/bin/python3 @@ -30883,15 +31301,17 @@ 199: 50# 0x00000000006B339E in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x00007FADFCF0DCA8 in /lib/x86_64-linux-gnu/libc.so.6 +199: 53# 0x00007F88346BCCA8 in /lib/x86_64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: .[03:35:43] +199: .[13:04:34] 199: 199: **** +213: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +213: 16777216 The "wavy" style of bond 1 was removed 199: Range Error 199: snapshotNum 199: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -30904,23 +31324,23 @@ 199: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 6# 0x00007FADFC76362C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 6# 0x00007F8833F1262C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x00007FADFA3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x00007FADFA3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x00007FADFA3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x00007FADFA3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 16# 0x00007FADFA3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x00007F88319B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x00007F88319B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x00007F88319B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x00007F88319B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 16# 0x00007F88319B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 22# 0x00007FADFC7603C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 22# 0x00007F8833F0F3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 23# _PyObject_MakeTpCall in /usr/bin/python3 199: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 25# 0x00000000005CBA19 in /usr/bin/python3 @@ -30952,13 +31372,13 @@ 199: 51# 0x00000000006B339E in /usr/bin/python3 199: 52# Py_RunMain in /usr/bin/python3 199: 53# Py_BytesMain in /usr/bin/python3 -199: 54# 0x00007FADFCF0DCA8 in /lib/x86_64-linux-gnu/libc.so.6 +199: 54# 0x00007F88346BCCA8 in /lib/x86_64-linux-gnu/libc.so.6 199: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 199: 56# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: [03:35:43] +199: [13:04:34] 199: 199: **** 199: Range Error @@ -30972,23 +31392,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x00007FADFC76362C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x00007F8833F1262C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x00007FADFA3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x00007FADFA3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x00007FADFA3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x00007FADFA3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x00007FADFA3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x00007F88319B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x00007F88319B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x00007F88319B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x00007F88319B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x00007F88319B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x00007FADFC7603C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x00007F8833F0F3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x00000000005CBA19 in /usr/bin/python3 @@ -31020,22 +31440,17 @@ 199: 50# 0x00000000006B339E in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x00007FADFCF0DCA8 in /lib/x86_64-linux-gnu/libc.so.6 +199: 53# 0x00007F88346BCCA8 in /lib/x86_64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- -169: ......... -169: ---------------------------------------------------------------------- -169: Ran 9 tests in 2.701s -169: -169: OK 199: **** 199: -199: .[03:35:43] +199: .[13:04:34] 199: 199: **** -197: ....[03:35:43] ERROR: Problems encountered parsing data fields -197: [03:35:43] ERROR: moving to the beginning of the next molecule +213: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +213: 16777216 The "wavy" style of bond 1 was removed 199: Range Error 199: snapshotNum 199: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -31048,23 +31463,23 @@ 199: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 6# 0x00007FADFC76362C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 6# 0x00007F8833F1262C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x00007FADFA3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x00007FADFA3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x00007FADFA3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x00007FADFA3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 16# 0x00007FADFA3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x00007F88319B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x00007F88319B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x00007F88319B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x00007F88319B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 16# 0x00007F88319B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 21# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 22# 0x00007FADFC7603C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 22# 0x00007F8833F0F3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 23# _PyObject_MakeTpCall in /usr/bin/python3 199: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 25# 0x00000000005CBA19 in /usr/bin/python3 @@ -31096,36 +31511,16 @@ 199: 51# 0x00000000006B339E in /usr/bin/python3 199: 52# Py_RunMain in /usr/bin/python3 199: 53# Py_BytesMain in /usr/bin/python3 -199: 54# 0x00007FADFCF0DCA8 in /lib/x86_64-linux-gnu/libc.so.6 +199: 54# 0x00007F88346BCCA8 in /lib/x86_64-linux-gnu/libc.so.6 199: 55# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 199: 56# _start in /usr/bin/python3 199: ---------- 199: **** 199: -197: [03:35:43] ERROR: Problems encountered parsing data fields -197: [03:35:43] ERROR: moving to the beginning of the next molecule -197: [03:35:43] Spurious data before the first property will be ignored -197: [03:35:43] Property will be truncated after the first blank line -199: [03:35:43] +199: [13:04:34] 199: 199: **** -197: [03:35:43] Property will be truncated after the first blank line -197: [03:35:43] Property will be truncated after the first blank line -197: [03:35:43] ERROR: Problems encountered parsing data fields -197: [03:35:43] ERROR: moving to the beginning of the next molecule -197: [03:35:43] ERROR: Problems encountered parsing data fields -197: [03:35:43] ERROR: moving to the beginning of the next molecule -197: [03:35:43] Spurious data before the first property will be ignored -197: [03:35:43] Property will be truncated after the first blank line -206: [03:35:43] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -197: [03:35:43] Property will be truncated after the first blank line -197: [03:35:43] Property will be truncated after the first blank line -197: [03:35:43] ERROR: Problems encountered parsing data fields -197: [03:35:43] ERROR: moving to the beginning of the next molecule -197: [03:35:43] Property will be truncated after the first blank line -197: [03:35:43] ERROR: Problems encountered parsing data fields -197: [03:35:43] ERROR: moving to the beginning of the next molecule -197: [03:35:43] Property will be truncated after the first blank line +213: 16777216 The "wavy" style of bond 4 was removed 199: Pre-condition Violation 199: d_dimension must be == 2 199: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp @@ -31137,23 +31532,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x00007FADFC76362C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x00007F8833F1262C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x00007FADFA3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x00007FADFA3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x00007FADFA3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x00007FADFA3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x00007FADFA3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x00007F88319B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x00007F88319B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x00007F88319B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x00007F88319B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x00007F88319B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x00007FADFC7603C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x00007F8833F0F3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x00000000005CBA19 in /usr/bin/python3 @@ -31185,13 +31580,13 @@ 199: 50# 0x00000000006B339E in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x00007FADFCF0DCA8 in /lib/x86_64-linux-gnu/libc.so.6 +199: 53# 0x00007F88346BCCA8 in /lib/x86_64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- 199: **** 199: -199: [03:35:43] +199: [13:04:34] 199: 199: **** 199: Pre-condition Violation @@ -31205,23 +31600,23 @@ 199: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitTrajectory.so.1 199: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdtrajectory.so 199: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 5# 0x00007FADFC76362C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 5# 0x00007F8833F1262C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 199: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 199: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 11# 0x00007FADFA3B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 12# 0x00007FADFA3B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 13# 0x00007FADFA3B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 14# 0x00007FADFA3B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -199: 15# 0x00007FADFA3B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 11# 0x00007F88319B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 12# 0x00007F88319B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 13# 0x00007F88319B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 14# 0x00007F88319B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +199: 15# 0x00007F88319B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 199: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 199: 20# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -199: 21# 0x00007FADFC7603C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +199: 21# 0x00007F8833F0F3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 199: 22# _PyObject_MakeTpCall in /usr/bin/python3 199: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 199: 24# 0x00000000005CBA19 in /usr/bin/python3 @@ -31253,7 +31648,7 @@ 199: 50# 0x00000000006B339E in /usr/bin/python3 199: 51# Py_RunMain in /usr/bin/python3 199: 52# Py_BytesMain in /usr/bin/python3 -199: 53# 0x00007FADFCF0DCA8 in /lib/x86_64-linux-gnu/libc.so.6 +199: 53# 0x00007F88346BCCA8 in /lib/x86_64-linux-gnu/libc.so.6 199: 54# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 199: 55# _start in /usr/bin/python3 199: ---------- @@ -31261,205 +31656,58 @@ 199: 199: . 199: ---------------------------------------------------------------------- -199: Ran 9 tests in 0.317s +199: Ran 9 tests in 1.000s 199: 199: OK 199: Testing Trajectory wrapper -202: .s. -202: ---------------------------------------------------------------------- -202: Ran 3 tests in 0.163s -202: -202: OK (skipped=1) -202: Testing Smiles and SD MultithreadedMolSupplier -197: .[03:35:43] SMILES Parse Error: syntax error while parsing: fail -197: [03:35:43] SMILES Parse Error: check for mistakes around position 1: -197: [03:35:43] fail -197: [03:35:43] ^ -197: [03:35:43] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -197: [03:35:43] ERROR: Smiles parse error on line 2 -197: [03:35:43] ERROR: Cannot create molecule from : 'fail' -197: >>> This may result in an infinite loop. It should finish almost instantly -197: <<< OK, it finished. -203: [03:35:43] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -203: [03:35:43] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -203: [03:35:43] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -203: .[03:35:43] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -203: [03:35:43] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -203: [03:35:43] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -203: ...[03:35:43] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -203: [03:35:43] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -203: [03:35:43] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -203: . -203: ---------------------------------------------------------------------- -203: Ran 5 tests in 0.015s -203: -203: OK -197: ............[03:35:43] Explicit valence for atom # 1 C, 5, is greater than permitted -40: [03:35:43] Finished -40: [03:35:43] testing github #1567: Non-canonical result from MolFragmentToSmiles() -40: [03:35:43] Finished -148: [03:35:43] Molecule does not have explicit Hs. Consider calling AddHs() -167/238 Test #40: hanoiTest .............................. Passed 6.21 sec -test 207 - Start 207: molValidateTest - -207: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest -207: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -207: Test timeout computed to be: 1500 -168/238 Test #199: pyTestTrajectory ....................... Passed 0.89 sec -test 208 - Start 208: molChargeTest - -208: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest -208: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -208: Test timeout computed to be: 1500 -197: ......[03:35:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -197: [03:35:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -197: [03:35:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -197: [03:35:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -169/238 Test #169: pyMMPA ................................. Passed 3.08 sec -test 209 - Start 209: molTautomerTest - -209: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest -209: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -209: Test timeout computed to be: 1500 -160: file testGithub4323_3.png gave hash 1732257634U not the expected 381907253U -197: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| -170/238 Test #203: pyTestPropertyLists .................... Passed 0.32 sec -160: [03:35:43] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. -test 210 - Start 210: molStandardizeSmallTest +213: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +213: 16777216 The "wavy" style of bond 3 was removed +174/238 Test #12: pyBV ................................... Passed 16.81 sec +test 216 + Start 216: pyScaffoldNetwork -210: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest -210: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -210: Test timeout computed to be: 1500 -171/238 Test #202: pyTestMultithreadedMolSupplier ......... Passed 0.64 sec -test 211 - Start 211: molFragmentTest +216: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" +216: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +216: Test timeout computed to be: 1500 +175/238 Test #204: pyCDXMLTest ............................ Passed 1.47 sec +test 217 + Start 217: pyScaffoldNetworkPickling -211: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest -211: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -211: Test timeout computed to be: 1500 -207: ERROR: [FeaturesValidation] Query atom 0 is not allowed -207: ERROR: [FeaturesValidation] Dummy atom 0 is not allowed -207: ERROR: [FeaturesValidation] Query bond 0 is not allowed -207: ERROR: [FeaturesValidation] Bond 0 of aromatic type is not allowed -207: ERROR: [FeaturesValidation] Bond 1 of aromatic type is not allowed -207: ERROR: [FeaturesValidation] Bond 2 of aromatic type is not allowed -207: ERROR: [FeaturesValidation] Bond 3 of aromatic type is not allowed -207: ERROR: [FeaturesValidation] Bond 5 of aromatic type is not allowed -207: ERROR: [FeaturesValidation] Bond 6 of aromatic type is not allowed -207: ERROR: [FeaturesValidation] Bond 2 of dative type is not allowed -207: ERROR: [FeaturesValidation] Bond 3 of dative type is not allowed -207: ERROR: [FeaturesValidation] Atom 2 with alias 'CF3' is not allowed -207: ERROR: [FeaturesValidation] Enhanced stereochemistry features are not allowed -207: ERROR: [StereoValidation] Atom 3 has both unknown and wedged/dashed stereo bonds. -207: here -207: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. -207: there -207: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. -172/238 Test #207: molValidateTest ........................ Passed 0.08 sec -test 212 - Start 212: molStandardizeCatchTest +217: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" +217: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +217: Test timeout computed to be: 1500 +213: 16777216 The representation of some functional groups was adjusted. +40: [13:04:34] Finished +40: [13:04:34] testing smiles round-tripping. +213: [13:04:34] Can't kekulize mol. Unkekulized atoms: 2 3 5 +213: =============================================================================== +213: All tests passed (268 assertions in 5 test cases) +213: +209: [13:04:34] Tautomer enumeration stopped at 292 tautomers: max transforms reached +176/238 Test #213: molStandardizePipelineTest ............. Passed 0.63 sec +test 218 + Start 218: testMolEnumerator -212: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest -212: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -212: Test timeout computed to be: 1500 -197: ........[03:35:43] non-ring atom 0 marked aromatic -197: [03:35:43] non-ring atom 0 marked aromatic -197: [03:35:43] -197: -197: **** -197: Range Error -197: idx -197: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -197: Failed Expression: 12 < 6 -197: ---------- -197: Stacktrace: -197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -197: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -197: 4# 0x00007F9C0CE84A30 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x00007F9C0F75062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -197: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so -197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x00007F9C0CDB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x00007F9C0CDB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x00007F9C0CDB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x00007F9C0CDB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 21# 0x00007F9C0CDB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 27# 0x00007F9C0F74D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 28# _PyObject_MakeTpCall in /usr/bin/python3 -197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 30# 0x00000000005CBA19 in /usr/bin/python3 -197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 32# 0x000000000068AE3F in /usr/bin/python3 -197: 33# 0x000000000062A0B0 in /usr/bin/python3 -197: 34# _PyObject_MakeTpCall in /usr/bin/python3 -197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 36# 0x00000000005CBA19 in /usr/bin/python3 -197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 38# 0x000000000068AE3F in /usr/bin/python3 -197: 39# 0x000000000062A0B0 in /usr/bin/python3 -197: 40# _PyObject_MakeTpCall in /usr/bin/python3 -197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 42# 0x00000000005CBA19 in /usr/bin/python3 -197: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 44# 0x000000000068AE3F in /usr/bin/python3 -197: 45# 0x000000000062A0B0 in /usr/bin/python3 -197: 46# _PyObject_MakeTpCall in /usr/bin/python3 -197: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 48# 0x000000000059F272 in /usr/bin/python3 -197: 49# _PyObject_MakeTpCall in /usr/bin/python3 -197: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 51# PyEval_EvalCode in /usr/bin/python3 -197: 52# 0x00000000006A5B71 in /usr/bin/python3 -197: 53# 0x00000000006A2C1E in /usr/bin/python3 -197: 54# 0x00000000006B3B53 in /usr/bin/python3 -197: 55# 0x00000000006B3563 in /usr/bin/python3 -197: 56# 0x00000000006B339E in /usr/bin/python3 -197: 57# Py_RunMain in /usr/bin/python3 -197: 58# Py_BytesMain in /usr/bin/python3 -197: 59# 0x00007F9C0FF38CA8 in /lib/x86_64-linux-gnu/libc.so.6 -197: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -197: 61# _start in /usr/bin/python3 -197: ---------- -197: **** -197: -197: [03:35:43] non-ring atom 0 marked aromatic -197: [03:35:43] non-ring atom 0 marked aromatic -197: [03:35:43] +218: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator +218: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator +218: Test timeout computed to be: 1500 +197: ............................[13:04:34] unable to set wavy bonds for double bonds: 3 +197: .............[13:04:34] 197: 197: **** 197: Range Error 197: idx 197: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -197: Failed Expression: 12 < 6 +197: Failed Expression: 6 < 5 197: ---------- 197: Stacktrace: 197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 197: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -197: 4# 0x00007F9C0CE84A30 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x00007F9C0F75062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 6# 0x00007F3EF36E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -31470,17 +31718,17 @@ 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x00007F9C0CDB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x00007F9C0CDB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x00007F9C0CDB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x00007F9C0CDB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 21# 0x00007F9C0CDB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x00007F3EF0DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x00007F3EF0DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x00007F3EF0DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x00007F3EF0DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 21# 0x00007F3EF0DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 27# 0x00007F9C0F74D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 27# 0x00007F3EF36E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 28# _PyObject_MakeTpCall in /usr/bin/python3 197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 30# 0x00000000005CBA19 in /usr/bin/python3 @@ -31512,364 +31760,220 @@ 197: 56# 0x00000000006B339E in /usr/bin/python3 197: 57# Py_RunMain in /usr/bin/python3 197: 58# Py_BytesMain in /usr/bin/python3 -197: 59# 0x00007F9C0FF38CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 59# 0x00007F3EF3ECFCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 61# _start in /usr/bin/python3 197: ---------- 197: **** 197: -173/238 Test #210: molStandardizeSmallTest ................ Passed 0.08 sec -test 213 - Start 213: molStandardizePipelineTest - -213: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest -213: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -213: Test timeout computed to be: 1500 -206: [03:35:43] Initializing Normalizer -206: [03:35:43] Running Normalizer -206: [03:35:43] Rule applied: BrokenazidetoN=N+=N- -206: [03:35:43] Initializing Normalizer -206: [03:35:43] Running Normalizer -206: [03:35:43] Initializing Normalizer -206: [03:35:43] Running Normalizer -174/238 Test #206: molNormalizeTest ....................... Passed 0.26 sec -test 214 - Start 214: pyMolStandardize - -214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" -214: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap -214: Test timeout computed to be: 1500 -197: ...............[03:35:43] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -197: [03:35:43] 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. -211: [03:35:43] SMARTS Parse Error: syntax error while parsing: [Cl -211: [03:35:43] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -175/238 Test #211: molFragmentTest ........................ Passed 0.08 sec -test 215 - Start 215: testScaffoldNetwork - -215: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork -215: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork -215: Test timeout computed to be: 1500 -213: Randomness seeded to: 29335413 -213: 1 Counts line too short: '' on line4 -213: 1 Could not instantiate a valid molecule from input -213: 8 Molecule has no atoms -213: [03:35:43] Explicit valence for atom # 1 N, 4, is greater than permitted -213: [03:35:43] Explicit valence for atom # 1 N, 4, is greater than permitted -176/238 Test #208: molChargeTest .......................... Passed 0.16 sec -test 216 - Start 216: pyScaffoldNetwork - -216: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" -216: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -216: Test timeout computed to be: 1500 -213: 8 Explicit valence for atom # 1 N, 4, is greater than permitted -213: 128 An error occurred while preparing the molecule for standardization. -213: 8 The molecule contains an unknown isotope: 3C -213: 4 Query atom 0 is not allowed -213: 4 Bond 0 of aromatic type is not allowed -213: 4 Bond 1 of aromatic type is not allowed -213: 4 Bond 2 of aromatic type is not allowed -213: 4 Bond 3 of aromatic type is not allowed -213: 4 Bond 5 of aromatic type is not allowed -213: 4 Bond 6 of aromatic type is not allowed -213: 4 Bond 2 of dative type is not allowed -213: 4 Bond 3 of dative type is not allowed -213: 4 Enhanced stereochemistry features are not allowed -213: 8 The radical at atom 0 is not allowed -213: [03:35:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -213: 16 The molecule includes non-null Z coordinates -197: ..............[03:35:43] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -197: [03:35:43] Explicit valence for atom # 1 C, 5, is greater than permitted -213: 32 Atom 0 too close to bond 2 -213: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit -213: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds -213: 64 Atom 0 has adjacent stereo bonds with like orientation -213: [03:35:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -213: 16 The molecule includes non-null Z coordinates -213: 64 Atom 0 has adjacent stereo bonds with like orientation -151: 789021579 -151: =============================================================================== -151: All tests passed (73 assertions in 3 test cases) -151: -213: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit -177/238 Test #151: molAlignCatchTest ...................... Passed 3.84 sec -test 217 - Start 217: pyScaffoldNetworkPickling - -217: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" -217: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -217: Test timeout computed to be: 1500 -213: 8388608 One or more metal atoms were disconnected. -213: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -213: 67108864 The protonation state was adjusted. -213: 16777216 The representation of some functional groups was adjusted. -213: 67108864 The protonation state was adjusted. -213: 16777216 The representation of some functional groups was adjusted. -213: 67108864 The protonation state was adjusted. -213: 16777216 The representation of some functional groups was adjusted. -213: 16777216 The representation of some functional groups was adjusted. -213: 67108864 The protonation state was adjusted. -213: 16777216 The representation of some functional groups was adjusted. -213: 67108864 The protonation state was adjusted. -213: 16777216 The representation of some functional groups was adjusted. -213: 67108864 The protonation state was adjusted. -213: 16777216 The representation of some functional groups was adjusted. -213: 67108864 The protonation state was adjusted. -213: 8388608 One or more metal atoms were disconnected. -213: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -204: . -204: ---------------------------------------------------------------------- -204: Ran 1 test in 0.024s -204: -204: OK -213: 67108864 The protonation state was adjusted. -213: 8388608 One or more metal atoms were disconnected. -213: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -213: 67108864 The protonation state was adjusted. -213: 8388608 One or more metal atoms were disconnected. -213: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -213: 67108864 The protonation state was adjusted. -213: 8388608 One or more metal atoms were disconnected. -213: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -213: 67108864 The protonation state was adjusted. -213: 8388608 One or more metal atoms were disconnected. -213: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -213: 67108864 The protonation state was adjusted. -213: 16777216 The "wavy" style of bond 4 was removed -213: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration -213: 16777216 The "wavy" style of bond 2 was removed -213: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -213: 16777216 The "wavy" style of bond 1 was removed -213: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -213: 16777216 The "wavy" style of bond 1 was removed -213: 16777216 The "wavy" style of bond 4 was removed -213: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -213: 16777216 The "wavy" style of bond 3 was removed -213: 16777216 The representation of some functional groups was adjusted. -213: [03:35:43] Can't kekulize mol. Unkekulized atoms: 2 3 5 -213: =============================================================================== -213: All tests passed (268 assertions in 5 test cases) -213: -178/238 Test #213: molStandardizePipelineTest ............. Passed 0.25 sec -test 218 - Start 218: testMolEnumerator - -218: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator -218: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator -218: Test timeout computed to be: 1500 -179/238 Test #204: pyCDXMLTest ............................ Passed 0.64 sec +148: [13:04:35] Molecule does not have explicit Hs. Consider calling AddHs() +177/238 Test #199: pyTestTrajectory ....................... Passed 2.29 sec test 219 Start 219: pyMolEnumerator 219: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 219: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 219: Test timeout computed to be: 1500 -160: file testFlexiCanvas.2a.png gave hash 1389326866U not the expected 2609920321U -160: file testFlexiCanvas.2b.png gave hash 614693993U not the expected 3615599154U -212: Randomness seeded to: 201673748 -212: * - * - * - * m1 -212: * - * - * - * m2 -160: file testFlexiCanvas.3.svg gave hash 236661785U not the expected 3544316588U -212: * - * - * - * m1 -212: * - * - * - * m2 -212: [03:35:43] Can't kekulize mol. Unkekulized atoms: 3 7 -212: [03:35:43] Can't kekulize mol. Unkekulized atoms: 3 8 -212: [03:35:43] Can't kekulize mol. Unkekulized atoms: 2 3 4 -218: Randomness seeded to: 3460664925 -218: [03:35:43] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -216: ....... -216: ---------------------------------------------------------------------- -216: Ran 7 tests in 0.049s -216: -216: OK +218: Randomness seeded to: 1254941687 +218: [13:04:35] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +69: [13:04:35] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +69: [13:04:35] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 217: . 217: ---------------------------------------------------------------------- -217: Ran 1 test in 0.031s +217: Ran 1 test in 0.016s 217: 217: OK 218: =============================================================================== 218: All tests passed (321 assertions in 16 test cases) 218: -180/238 Test #218: testMolEnumerator ...................... Passed 0.20 sec +178/238 Test #218: testMolEnumerator ...................... Passed 0.44 sec test 220 Start 220: testAbbreviations 220: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 220: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations 220: 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 -181/238 Test #216: pyScaffoldNetwork ...................... Passed 0.41 sec +179/238 Test #217: pyScaffoldNetworkPickling .............. Passed 0.58 sec test 221 Start 221: pyAbbreviations 221: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 221: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 221: Test timeout computed to be: 1500 -160: file testGithub4764.sz1.png gave hash 517897906U not the expected 2179222277U -182/238 Test #217: pyScaffoldNetworkPickling .............. Passed 0.39 sec +180/238 Test #42: resMolSupplierTest ..................... Passed 17.06 sec test 222 Start 222: generalizedSubstructCatch 222: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 222: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 222: Test timeout computed to be: 1500 -160: file testGithub4764.sz2.png gave hash 2568067924U not the expected 444262090U -220: Randomness seeded to: 3473190173 -220: [03:35:43] SMARTS Parse Error: syntax error while parsing: *fail -220: [03:35:43] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -220: [03:35:43] no suitable SubstanceGroups found -220: =============================================================================== -220: All tests passed (195 assertions in 12 test cases) -220: -183/238 Test #220: testAbbreviations ...................... Passed 0.10 sec +69: [13:04:35] Empty atom list: 'M ALS 1 0 F' on line 8. +220: Randomness seeded to: 97257887 +220: [13:04:35] SMARTS Parse Error: syntax error while parsing: *fail +220: [13:04:35] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +181/238 Test #69: fileParsersTest1 ....................... Passed 16.75 sec test 223 Start 223: pyGeneralizedSubstruct 223: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 223: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 223: Test timeout computed to be: 1500 -197: ............................[03:35:43] unable to set wavy bonds for double bonds: 3 -219: ... -219: ---------------------------------------------------------------------- -219: Ran 3 tests in 0.016s -219: -219: OK -197: .............[03:35:44] -197: -197: **** -197: Range Error -197: idx -197: Violation occurred on line 209 in file ./Code/GraphMol/ROMol.cpp -197: Failed Expression: 6 < 5 -197: ---------- -197: Stacktrace: -197: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -197: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 -197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -197: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -197: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 6# 0x00007F9C0F75062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so -197: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -197: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so -197: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -197: 12# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdDepictor.so -197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so -197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -197: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x00007F9C0CDB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x00007F9C0CDB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x00007F9C0CDB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x00007F9C0CDB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 21# 0x00007F9C0CDB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so -197: 26# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 27# 0x00007F9C0F74D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 28# _PyObject_MakeTpCall in /usr/bin/python3 -197: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 30# 0x00000000005CBA19 in /usr/bin/python3 -197: 31# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 32# 0x000000000068AE3F in /usr/bin/python3 -197: 33# 0x000000000062A0B0 in /usr/bin/python3 -197: 34# _PyObject_MakeTpCall in /usr/bin/python3 -197: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 36# 0x00000000005CBA19 in /usr/bin/python3 -197: 37# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 38# 0x000000000068AE3F in /usr/bin/python3 -197: 39# 0x000000000062A0B0 in /usr/bin/python3 -197: 40# _PyObject_MakeTpCall in /usr/bin/python3 -197: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 42# 0x00000000005CBA19 in /usr/bin/python3 -197: 43# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 44# 0x000000000068AE3F in /usr/bin/python3 -197: 45# 0x000000000062A0B0 in /usr/bin/python3 -197: 46# _PyObject_MakeTpCall in /usr/bin/python3 -197: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 48# 0x000000000059F272 in /usr/bin/python3 -197: 49# _PyObject_MakeTpCall in /usr/bin/python3 -197: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -197: 51# PyEval_EvalCode in /usr/bin/python3 -197: 52# 0x00000000006A5B71 in /usr/bin/python3 -197: 53# 0x00000000006A2C1E in /usr/bin/python3 -197: 54# 0x00000000006B3B53 in /usr/bin/python3 -197: 55# 0x00000000006B3563 in /usr/bin/python3 -197: 56# 0x00000000006B339E in /usr/bin/python3 -197: 57# Py_RunMain in /usr/bin/python3 -197: 58# Py_BytesMain in /usr/bin/python3 -197: 59# 0x00007F9C0FF38CA8 in /lib/x86_64-linux-gnu/libc.so.6 -197: 60# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -197: 61# _start in /usr/bin/python3 -197: ---------- -197: **** -197: -160: file testGithub4764.sz3.png gave hash 2910755141U not the expected 3567162200U -184/238 Test #219: pyMolEnumerator ........................ Passed 0.37 sec +40: [13:04:35] Finished +40: [13:04:35] testing github #1567: Non-canonical result from MolFragmentToSmiles() +40: [13:04:35] Finished +212: Randomness seeded to: 1923890598 +212: * - * - * - * m1 +182/238 Test #40: hanoiTest .............................. Passed 17.20 sec test 224 Start 224: testMolProcessing 224: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing 224: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing 224: Test timeout computed to be: 1500 -185/238 Test #42: resMolSupplierTest ..................... Passed 7.01 sec +220: [13:04:35] no suitable SubstanceGroups found +220: =============================================================================== +220: All tests passed (195 assertions in 12 test cases) +220: +183/238 Test #220: testAbbreviations ...................... Passed 0.20 sec test 225 Start 225: pyMolProcessing 225: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" 225: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolProcessing/Wrap 225: 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 -160: file github5383_1.png gave hash 1118153320U not the expected 2893520928U -160: file acs1996_1.png gave hash 1014030062U not the expected 2329725800U -221: ....... -221: ---------------------------------------------------------------------- -221: Ran 7 tests in 0.023s -221: -221: OK -160: file acs1996_2.png gave hash 1604110899U not the expected 2996350718U -160: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U -209: [03:35:44] Tautomer enumeration stopped at 292 tautomers: max transforms reached -186/238 Test #221: pyAbbreviations ........................ Passed 0.34 sec +212: * - * - * - * m2 +212: * - * - * - * m1 +212: * - * - * - * m2 +212: [13:04:35] Can't kekulize mol. Unkekulized atoms: 3 7 +212: [13:04:35] Can't kekulize mol. Unkekulized atoms: 3 8 +169: ......... +169: ---------------------------------------------------------------------- +169: Ran 9 tests in 10.017s +169: +169: OK +212: [13:04:35] Can't kekulize mol. Unkekulized atoms: 2 3 4 +160: file testFlexiCanvas.2a.png gave hash 1389326866U not the expected 2609920321U +160: file testFlexiCanvas.2b.png gave hash 614693993U not the expected 3615599154U +209: [13:04:35] Tautomer enumeration stopped at 292 tautomers: max transforms reached +160: file testFlexiCanvas.3.svg gave hash 236661785U not the expected 3544316588U +148: [13:04:35] Molecule does not have explicit Hs. Consider calling AddHs() +209: [13:04:35] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +184/238 Test #169: pyMMPA ................................. Passed 11.40 sec test 226 Start 226: testMIF 226: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF 226: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields 226: Test timeout computed to be: 1500 -160: [03:35:44] 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 -117: =>start test GETAWAY custom -148: [03:35:44] Molecule does not have explicit Hs. Consider calling AddHs() -117: [03:35:44] test on : 365 molecules done -187/238 Test #117: testRDFcustom .......................... Passed 6.84 sec -222: Randomness seeded to: 4116901240 -222: =============================================================================== -222: All tests passed (486 assertions in 10 test cases) -222: +221: ....... +221: ---------------------------------------------------------------------- +221: Ran 7 tests in 0.057s +221: +221: OK +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 +128: [13:04:36] done +128: [13:04:36] ------------------------------------- +128: [13:04:36] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +128: [13:04:36] done +128: [13:04:36] ------------------------------------- +128: [13:04:36] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +128: [13:04:36] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:36] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] done +128: [13:04:36] ------------------------------------- +128: [13:04:36] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +128: [13:04:36] done +128: [13:04:36] ------------------------------------- +128: [13:04:36] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] done +128: [13:04:36] ------------------------------------- +128: [13:04:36] Test unfolded version of RDKFP +128: [13:04:36] ------------------------------------- +128: [13:04:36] 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: [13:04:36] ------------------------------------- +128: [13:04:36] Single atoms setting radius 1 bits in Morgan fingerprints +128: [13:04:36] done +128: [13:04:36] ------------------------------------- +128: [13:04:36] Github #879: Pattern fingerprint should set bits for single-atom fragments. +128: [13:04:36] done +128: [13:04:36] ------------------------------------- +128: [13:04:36] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +128: [13:04:36] done +128: [13:04:36] ------------------------------------- +128: [13:04:36] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +128: [13:04:36] done +128: [13:04:36] ------------------------------------- +128: [13:04:36] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +128: [13:04:36] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:36] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:36] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:36] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:36] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:36] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:36] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:36] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:36] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:36] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:36] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:36] DEPRECATION WARNING: please use AtomPairGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [13:04:36] done +128: [13:04:36] ------------------------------------- +128: [13:04:36] Github #2115: BitInfo not complete for RDKFingerprint +160: file testGithub4764.sz1.png gave hash 517897906U not the expected 2179222277U +128: [13:04:36] done +128: [13:04:36] ------------------------------------- +128: [13:04:36] Github #3723: Fingerprint crash for mols with Zero order bonds +128: [13:04:36] done +185/238 Test #128: testFingerprints ....................... Passed 13.85 sec test 227 Start 227: pyMIF 227: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" 227: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap 227: Test timeout computed to be: 1500 -188/238 Test #222: generalizedSubstructCatch .............. Passed 0.40 sec +222: Randomness seeded to: 3599161135 +222: =============================================================================== +222: All tests passed (486 assertions in 10 test cases) +222: +170: Randomness seeded to: 1705113478 +170: [13:04:36] Timed out after 11 seconds. +186/238 Test #222: generalizedSubstructCatch .............. Passed 0.70 sec test 228 Start 228: testQuery 228: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Query/testQuery 228: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Query 228: Test timeout computed to be: 1500 -214: .....[03:35:44] Tautomer enumeration stopped at 292 tautomers: max transforms reached -146: validating reference data 228: Query 228: Query2 228: Equality @@ -31887,13 +31991,20 @@ 228: XOr 228: pointer and copy foo 228: Set2 -189/238 Test #228: testQuery .............................. Passed 0.02 sec +187/238 Test #228: testQuery .............................. Passed 0.03 sec test 229 Start 229: testBaseFeatures 229: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features/testBaseFeatures 229: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/Features 229: Test timeout computed to be: 1500 +188/238 Test #221: pyAbbreviations ........................ Passed 0.76 sec +test 230 + Start 230: testMatCalc + +230: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc +230: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc +230: Test timeout computed to be: 1500 229: ------------------------------------- 229: Basics for ExplicitFeatures. 229: done @@ -31903,18 +32014,6 @@ 229: ------------------------------------- 229: ExplicitFeatures 2D, string type. 229: done -190/238 Test #229: testBaseFeatures ....................... Passed 0.01 sec -test 230 - Start 230: testMatCalc - -230: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc -230: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc -230: Test timeout computed to be: 1500 -226: Randomness seeded to: 89267843 -226: =============================================================================== -226: All tests passed (27926 assertions in 8 test cases) -226: -191/238 Test #226: testMIF ................................ Passed 0.16 sec 230: 1.68022e+08 230: 1.73149e+08 230: 1.05549e+08 @@ -31960,110 +32059,120 @@ 230: 9.49496e+07 230: 2.25618e+08 230: 1.30219e+08 +160: file testGithub4764.sz2.png gave hash 2568067924U not the expected 444262090U +189/238 Test #229: testBaseFeatures ....................... Passed 0.04 sec +190/238 Test #230: testMatCalc ............................ Passed 0.02 sec test 231 Start 231: pyMatCalc 231: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 231: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 231: Test timeout computed to be: 1500 -192/238 Test #230: testMatCalc ............................ Passed 0.02 sec test 232 Start 232: testSimDivPickers 232: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/testSimDivPickers 232: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers 232: Test timeout computed to be: 1500 -232: [03:35:44] ------------------------------------- -232: [03:35:44] Testing github issue 1421: MaxMinPicker picking non-existent element. -232: [03:35:44] Done -232: [03:35:44] ------------------------------------- -232: [03:35:44] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -232: [03:35:44] Done -193/238 Test #232: testSimDivPickers ...................... Passed 0.01 sec +219: ... +219: ---------------------------------------------------------------------- +219: Ran 3 tests in 0.048s +219: +219: OK +232: [13:04:36] ------------------------------------- +232: [13:04:36] Testing github issue 1421: MaxMinPicker picking non-existent element. +232: [13:04:36] Done +232: [13:04:36] ------------------------------------- +232: [13:04:36] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +232: [13:04:36] Done +191/238 Test #232: testSimDivPickers ...................... Passed 0.03 sec test 233 Start 233: pickersTestsCatch 233: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 233: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers 233: Test timeout computed to be: 1500 -214: [03:35:44] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -148: [03:35:44] Molecule does not have explicit Hs. Consider calling AddHs() -160: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U -194/238 Test #205: molStandardizeTest ..................... Passed 1.50 sec +216: ....... +216: ---------------------------------------------------------------------- +216: Ran 7 tests in 0.206s +216: +216: OK +226: Randomness seeded to: 3061650431 +226: =============================================================================== +226: All tests passed (27926 assertions in 8 test cases) +226: +192/238 Test #226: testMIF ................................ Passed 0.35 sec test 234 Start 234: pySimDivPickers 234: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/SimDivPickers/Wrap/testPickers.py" 234: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap 234: Test timeout computed to be: 1500 -233: Randomness seeded to: 256699394 -233: =============================================================================== -233: All tests passed (21267 assertions in 1 test case) -233: -195/238 Test #233: pickersTestsCatch ...................... Passed 0.16 sec +209: [13:04:36] Tautomer enumeration stopped at 32 tautomers: canceled +209: Enumeration was canceled due to timeout (50 ms) +193/238 Test #219: pyMolEnumerator ........................ Passed 1.31 sec test 235 Start 235: pyRanker 235: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ML/InfoTheory/Wrap/testRanker.py" 235: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap 235: Test timeout computed to be: 1500 -148: [03:35:44] Molecule does not have explicit Hs. Consider calling AddHs() -214: .[03:35:44] Tautomer enumeration stopped at 43 tautomers: canceled -214: Enumeration was canceled due to timeout (50 ms) -227: ....... -227: ---------------------------------------------------------------------- -227: Ran 7 tests in 0.102s -227: -227: OK -227: Testing MIF wrapper -163: [03:35:44] The provided InitialSeed is not an MCS and will be ignored -148: [03:35:44] Molecule does not have explicit Hs. Consider calling AddHs() -189: .................... -189: ---------------------------------------------------------------------- -189: Ran 20 tests in 3.143s -189: -189: OK -196/238 Test #227: pyMIF .................................. Passed 0.52 sec +148: [13:04:36] Molecule does not have explicit Hs. Consider calling AddHs() +160: file testGithub4764.sz3.png gave hash 2910755141U not the expected 3567162200U +146: processing +146: launch :0 +146: launch :1 +146: launch :2 +146: launch :3 +160: file github5383_1.svg gave hash 4241964660U not the expected 1815941817U +233: Randomness seeded to: 2405668826 +233: =============================================================================== +233: All tests passed (21267 assertions in 1 test case) +233: +194/238 Test #233: pickersTestsCatch ...................... Passed 0.29 sec test 236 Start 236: testChemicalFeatures 236: Test command: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures 236: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures 236: Test timeout computed to be: 1500 +160: file github5383_2.svg gave hash 2560846108U not the expected 0U 236: ----------------------------------------- 236: Test1 236: Done -197/238 Test #236: testChemicalFeatures ................... Passed 0.01 sec +195/238 Test #236: testChemicalFeatures ................... Passed 0.02 sec test 237 Start 237: pyFeatures 237: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202503.1/Code/ChemicalFeatures/Wrap/testFeatures.py" 237: Working Directory: /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap 237: Test timeout computed to be: 1500 -198/238 Test #189: pyRGroupDecomposition .................. Passed 3.51 sec +160: file github5383_1.png gave hash 1118153320U not the expected 2893520928U +160: file acs1996_1.png gave hash 1014030062U not the expected 2329725800U +160: file acs1996_2.png gave hash 1604110899U not the expected 2996350718U +160: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U +196/238 Test #216: pyScaffoldNetwork ...................... Passed 1.75 sec test 238 Start 238: pythonProjectTests 238: Test command: /usr/bin/python3 "-m" "pytest" 238: Working Directory: /build/reproducible-path/rdkit-202503.1/Projects 238: Test timeout computed to be: 1500 -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -209: [03:35:44] Tautomer enumeration stopped at 292 tautomers: max transforms reached +160: [13:04:36] 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 225: .. 225: ---------------------------------------------------------------------- -225: Ran 2 tests in 0.287s +225: Ran 2 tests in 0.373s 225: 225: OK -186: iterative -160: file AtropManyChiralsEnhanced.svg gave hash 3443464321U not the expected 2256768013U -29: All 191 tests passed -199/238 Test #225: pyMolProcessing ........................ Passed 0.90 sec -148: [03:35:45] Molecule does not have explicit Hs. Consider calling AddHs() -209: [03:35:45] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -171: Randomness seeded to: 2630812898 -171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -234: [03:35:45] the useCache argument is deprecated and ignored -235: ..[03:35:45] +223: ....... +223: ---------------------------------------------------------------------- +223: Ran 7 tests in 0.502s +223: +223: OK +197/238 Test #223: pyGeneralizedSubstruct ................. Passed 1.40 sec +198/238 Test #225: pyMolProcessing ........................ Passed 1.49 sec +235: ..[13:04:37] 235: 235: **** 235: Invariant Violation @@ -32078,14 +32187,14 @@ 235: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 235: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 235: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -235: 6# 0x00007F76529DF62C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +235: 6# 0x00007F219499162C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 235: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 235: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 235: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 235: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 235: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 235: 12# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -235: 13# 0x00007F76529DC3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +235: 13# 0x00007F219498E3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 235: 14# _PyObject_MakeTpCall in /usr/bin/python3 235: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 235: 16# 0x00000000005CBA19 in /usr/bin/python3 @@ -32117,7 +32226,7 @@ 235: 42# 0x00000000006B339E in /usr/bin/python3 235: 43# Py_RunMain in /usr/bin/python3 235: 44# Py_BytesMain in /usr/bin/python3 -235: 45# 0x00007F76547C4CA8 in /lib/x86_64-linux-gnu/libc.so.6 +235: 45# 0x00007F219615ACA8 in /lib/x86_64-linux-gnu/libc.so.6 235: 46# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 235: 47# _start in /usr/bin/python3 235: ---------- @@ -32125,48 +32234,65 @@ 235: 235: ... 235: ---------------------------------------------------------------------- -235: Ran 5 tests in 0.053s +235: Ran 5 tests in 0.032s 235: 235: OK -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -200/238 Test #235: pyRanker ............................... Passed 0.60 sec -160: file testGithub_7739_1.svg gave hash 3358510977U not the expected 2615562225U +160: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U +227: ....... +227: ---------------------------------------------------------------------- +227: Ran 7 tests in 0.173s +227: +227: OK +227: Testing MIF wrapper +117: =>start test GETAWAY custom +117: [13:04:37] test on : 365 molecules done +199/238 Test #227: pyMIF .................................. Passed 1.04 sec +200/238 Test #117: testRDFcustom .......................... Passed 17.60 sec +201/238 Test #235: pyRanker ............................... Passed 0.82 sec +234: [13:04:37] the useCache argument is deprecated and ignored +209: 375 +209: Enumeration has completed +209: [13:04:37] Tautomer enumeration stopped at 51 tautomers: canceled +202/238 Test #205: molStandardizeTest ..................... Passed 4.17 sec +214: .....[13:04:37] Tautomer enumeration stopped at 292 tautomers: max transforms reached +234: ...[13:04:37] the useCache argument is deprecated and ignored +234: [13:04:37] the useCache argument is deprecated and ignored +234: .[13:04:37] the useCache argument is deprecated and ignored +160: file AtropManyChiralsEnhanced.svg gave hash 3443464321U not the expected 2256768013U 237: .. 237: ---------------------------------------------------------------------- -237: Ran 2 tests in 0.002s +237: Ran 2 tests in 0.021s 237: 237: OK -160: file testGithub_7739_3.svg gave hash 176211825U not the expected 1037942338U 237: Testing ChemicalFeatures Wrapper code: -148: [03:35:45] Molecule does not have explicit Hs. Consider calling AddHs() +214: [13:04:38] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +231: ..... +231: ---------------------------------------------------------------------- +231: Ran 5 tests in 1.061s +231: +231: OK +203/238 Test #237: pyFeatures ............................. Passed 1.69 sec +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 -201/238 Test #237: pyFeatures ............................. Passed 0.37 sec 160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U -223: ....... -223: ---------------------------------------------------------------------- -223: Ran 7 tests in 0.615s -223: -223: OK -202/238 Test #223: pyGeneralizedSubstruct ................. Passed 1.36 sec +204/238 Test #231: pyMatCalc .............................. Passed 4.03 sec +197: ....................[13:04:40] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [13:04:40] Explicit valence for atom # 6 F, 2, is greater than permitted +197: [13:04:40] Can't kekulize mol. Unkekulized atoms: 3 4 5 160: =============================================================================== 160: All tests passed (6857 assertions in 116 test cases) 160: -203/238 Test #160: moldraw2DTestCatch ..................... Passed 5.43 sec -234: ...[03:35:45] the useCache argument is deprecated and ignored -234: [03:35:45] the useCache argument is deprecated and ignored -234: .[03:35:45] the useCache argument is deprecated and ignored -231: ..... -231: ---------------------------------------------------------------------- -231: Ran 5 tests in 0.540s -231: -231: OK -204/238 Test #231: pyMatCalc .............................. Passed 1.05 sec -209: [03:35:45] Tautomer enumeration stopped at 59 tautomers: canceled -209: Enumeration was canceled due to timeout (50 ms) -128: [03:35:45] done -128: [03:35:45] ------------------------------------- -128: [03:35:45] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +205/238 Test #160: moldraw2DTestCatch ..................... Passed 16.35 sec +148: .[13:04:40] Molecule does not have explicit Hs. Consider calling AddHs() +186: iterative +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +197: .................[13:04:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +171: Randomness seeded to: 1774604925 +171: /build/reproducible-path/rdkit-202503.1/Code/GraphMol/RascalMCES/data/chembl_1907596.smi +29: All 191 tests passed +214: .[13:04:40] Tautomer enumeration stopped at 20 tautomers: canceled +214: Enumeration was canceled due to timeout (50 ms) 150: *********************************************************** 150: Testing O3AAlign 150: --------------------------------- @@ -32197,157 +32323,1087 @@ 150: testMMFFO3A multithreading 150: 150: generating reference data -128: [03:35:45] done -128: [03:35:45] ------------------------------------- -128: [03:35:45] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -128: [03:35:45] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:45] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] done -128: [03:35:45] ------------------------------------- -128: [03:35:45] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -128: [03:35:45] done -128: [03:35:45] ------------------------------------- -128: [03:35:45] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] done -128: [03:35:45] ------------------------------------- -128: [03:35:45] Test unfolded version of RDKFP -128: [03:35:45] ------------------------------------- -128: [03:35:45] Test bitinfo of RDKFP -128: 562: [ 2 ], -128: 709: [ 0 1 ], -128: 1118: [ 0 1 2 ], -128: 1183: [ 1 2 ], -128: 1233: [ 0 1 2 ], -128: 1308: [ 0 ], [ 1 ], -128: 1339: [ 2 ], -128: 1728: [ 1 2 ], -128: 1772: [ 0 ], [ 1 ], -128: 1813: [ 0 1 ], -128: ------------ -128: [03:35:45] ------------------------------------- -128: [03:35:45] Single atoms setting radius 1 bits in Morgan fingerprints -128: [03:35:45] done -128: [03:35:45] ------------------------------------- -128: [03:35:45] Github #879: Pattern fingerprint should set bits for single-atom fragments. -128: [03:35:45] done -128: [03:35:45] ------------------------------------- -128: [03:35:45] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -128: [03:35:45] done -128: [03:35:45] ------------------------------------- -128: [03:35:45] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -128: [03:35:45] done -128: [03:35:45] ------------------------------------- -128: [03:35:45] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -128: [03:35:45] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:45] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:45] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:45] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:45] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:45] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:45] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:45] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:45] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:45] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:45] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:45] DEPRECATION WARNING: please use AtomPairGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [03:35:45] done -128: [03:35:45] ------------------------------------- -128: [03:35:45] Github #2115: BitInfo not complete for RDKFingerprint -128: [03:35:45] done -128: [03:35:45] ------------------------------------- -128: [03:35:45] Github #3723: Fingerprint crash for mols with Zero order bonds -128: [03:35:45] done -205/238 Test #128: testFingerprints ....................... Passed 7.84 sec -186: bulk -215: Randomness seeded to: 3704316543 +183: [13:04:41] ------------------------------------- +183: [13:04:41] testing PatternHolder +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +209: CN=c1cc[nH]cn1 +209: CN=c1ccnc[nH]1 +209: CNc1ccncn1 +209: res: CNc1ccncn1 +209: CN=c1cccc[nH]1 +209: CNc1ccccn1 +209: res: CNc1ccccn1 +163: [13:04:41] The provided InitialSeed is not an MCS and will be ignored +183: [13:04:42] ------------------------------------- +183: [13:04:42] testing TautomerPatternHolder +215: Randomness seeded to: 3587469190 215: =============================================================================== 215: All tests passed (273 assertions in 19 test cases) 215: -206/238 Test #215: testScaffoldNetwork .................... Passed 2.60 sec -148: .[03:35:46] Molecule does not have explicit Hs. Consider calling AddHs() -197: ....................[03:35:46] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [03:35:46] Explicit valence for atom # 6 F, 2, is greater than permitted -197: [03:35:46] Can't kekulize mol. Unkekulized atoms: 3 4 5 -197: .................[03:35:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -164: ........................................[03:35:48] The provided InitialSeed is not an MCS and will be ignored -164: [03:35:48] The provided InitialSeed is not an MCS and will be ignored -164: [03:35:48] The provided InitialSeed is not an MCS and will be ignored 125: Warning: Atom Count for residue GLU5A does not match expected count 125: Warning: Atom Count for residue ASN39A does not match expected count +206/238 Test #215: testScaffoldNetwork .................... Passed 7.92 sec 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 -164: .[03:35:48] The provided InitialSeed is not an MCS and will be ignored 125: Warning: Atom Count for residue GLU150A does not match expected count 125: Warning: Atom Count for residue ASN157A does not match expected count -164: [03:35:48] The provided InitialSeed is not an MCS and will be ignored -164: [03:35:48] The provided InitialSeed is not an MCS and will be ignored -186: bulk, no symmetry -164: .[03:35:48] The provided InitialSeed is not an MCS and will be ignored -164: [03:35:48] The provided InitialSeed is not an MCS and will be ignored -164: [03:35:48] The provided InitialSeed is not an MCS and will be ignored -146: processing -146: launch :0 -146: launch :1 -146: launch :2 -146: launch :3 -164: .[03:35:48] The provided InitialSeed is not an MCS and will be ignored 125: =============================================================================== 125: All tests passed (515 assertions in 10 test cases) 125: -207/238 Test #125: descriptorsTestCatch ................... Passed 10.54 sec -164: [03:35:48] The provided InitialSeed is not an MCS and will be ignored -164: [03:35:48] The provided InitialSeed is not an MCS and will be ignored -173: [03:35:48] Building the fingerprints may take some time. -209: 375 -209: Enumeration has completed -164: ................. -164: ---------------------------------------------------------------------- -164: Ran 60 tests in 7.785s -164: -164: OK -150: processing -150: launch :0 -150: launch :1 -150: launch :2 -150: launch :3 -209: [03:35:48] Tautomer enumeration stopped at 32 tautomers: canceled -208/238 Test #164: pyFMCS ................................. Passed 8.46 sec +207/238 Test #125: descriptorsTestCatch ................... Passed 22.61 sec +208/238 Test #209: molTautomerTest ........................ Passed 8.68 sec +173: [13:04:42] Building the fingerprints may take some time. +183: [13:04:42] ------------------------------------- +183: [13:04:42] testSegFaultInHolder +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] [13:04:42] [13:04:42] [13:04:42] [13:04:42] [13:04:42] [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] [13:04:42] SMILES Parse Error: syntax error while parsing: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf[13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] [13:04:42] [13:04:42] [13:04:42] [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: syntax error[13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: [13:04:42] syntax error while parsing: dsafsdf +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdfSMILES Parse Error: syntax error while parsing: dsafsdf +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] +183: dsafsdf +183: [13:04:42] ^syntax error[13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1[13:04:42] SMILES[13:04:42] ^ while parsing: [13:04:42] dsafsdf +183: +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1:: +183: +183: [13:04:42] [13:04:42] dsafsdf[13:04:42] +183: Parse Error: [13:04:42] ^SMILES +183: Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf +183: SMILES Parse Error: [13:04:42] ^ for input: 'syntax errorFailed parsing SMILES 'dsafsdf' while parsing: dsafsdfdsafsdf for input: '[13:04:42] dsafsdf'SMILES +183: +183: ' +183: Parse Error: Failed parsing SMILES 'dsafsdf' +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^[13:04:42] SMILES Parse Error: +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[13:04:42] [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf +183: ' +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: ' for input: '[13:04:42] SMILES Parse Error: syntax errordsafsdf' +183: while parsing: dsafsdf +183: dsafsdf' +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] [13:04:42] SMILESSMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] Parse Error: [13:04:42] SMILES Parse Error: check for mistakes around position [13:04:42] dsafsdf +183: [13:04:42] ^ +183: SMILES Parse Error: check for mistakes around position Failed parsing SMILES 'dsafsdf'[13:04:42] SMILESSMILES Parse Error: Failed parsing SMILES 'dsafsdf' Parse Error: 1: +183: [13:04:42] dsafsdfFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: for input: 'dsafsdf' +183: [13:04:42] ^ +183: for input: 'dsafsdf[13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: ' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1:[13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: [13:04:42] [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] [13:04:42] [13:04:42] [13:04:42] SMILES Parse Error: syntax error[13:04:42] while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] syntax errorSMILES Parse Error: syntax error while parsing: dsafsdf[13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] [13:04:42] [13:04:42] [13:04:42] [13:04:42] SMILES Parse Error: syntax errorSMILES Parse Error: [13:04:42] syntax error while parsing: SMILES Parse Error: syntax error while parsing: [13:04:42] [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf[13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: [13:04:42] [13:04:42] SMILES Parse Error: SMILES Parse Error: syntax errorsyntax error while parsing: dsafsdf +183: [13:04:42] [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] SMILES Parse Error: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: SMILES Parse Error: syntax error while parsing: dsafsdf while parsing: +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1[13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: dsafsdf[13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] [13:04:42] SMILES Parse Error: : +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [13:04:42] dsafsdf[13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfdsafsdf +183: +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] [13:04:42] SMILES^ +183: SMILES Parse Error: check for mistakes around position syntax error while parsing: [13:04:42] 1:dsafsdf +183: Parse Error: [13:04:42] +183: [13:04:42] [13:04:42] SMILESdsafsdf +183: [13:04:42] ' +183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf'SMILES Parse Error: check for mistakes around position 1: +183: +183: ' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf[13:04:42] SMILES Parse Error: syntax error[13:04:42] SMILES Parse Error: check for mistakes around position +183: while parsing: dsafsdf1: +183: [13:04:42] SMILES Parse Error: check for mistakes around position dsafsdf +183: +183: [13:04:42] 1[13:04:42] dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position : +183: [13:04:42] [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] [13:04:42] SMILES Parse Error: syntax errorsyntax error[13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +74: [13:04:42] Finished: testSmiCorrectness() +74: [13:04:42] ----------------------------------------- +74: +74: [13:04:42] +74: ----------------------------------------- +183: SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf +183: +183: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: syntax error while parsing: dsafsdf[13:04:42] +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] SMILES Parse Error: ^ +183: syntax errorsyntax error[13:04:42] while parsing: SMILES Parse Error: syntax error while parsing: while parsing: syntax error while parsing: dsafsdfdsafsdfdsafsdfdsafsdf +183: +183: +183: [13:04:42] [13:04:42] +183: SMILES[13:04:42] [13:04:42] SMILES Parse Error: check for mistakes around position while parsing: 1dsafsdfSMILES Parse Error: check for mistakes around position Parse Error: +183: 1:[13:04:42] +183: SMILES Parse Error: check for mistakes around position Failed parsing SMILES 'dsafsdf'1:SMILES Parse Error: check for mistakes around position for input: '[13:04:42] :SMILES Parse Error: check for mistakes around position +183: [13:04:42] +183: 11:dsafsdf +183: [13:04:42] dsafsdf +183: [13:04:42] [13:04:42] ^:[13:04:42] +183: dsafsdf +183: dsafsdf[13:04:42] ^ +183: [13:04:42] dsafsdf' +183: [13:04:42] +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[13:04:42] ^ +183: for input: 'dsafsdf' +183: +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: while parsing: dsafsdf +183: [13:04:42] [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +74: [13:04:42] Spurious data before the first property will be ignored +74: [13:04:42] Property will be truncated after the first blank line +74: [13:04:42] Property will be truncated after the first blank line +74: [13:04:42] Property will be truncated after the first blank line +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] SMILES Parse Error: syntax error while parsing: dsafsdf +183: [13:04:42] SMILES Parse Error: check for mistakes around position 1: +183: [13:04:42] dsafsdf +183: [13:04:42] ^ +183: [13:04:42] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +183: [13:04:42] ------------------------------------- +183: [13:04:42] Results do not depend on numThreads +164: ........................................[13:04:43] The provided InitialSeed is not an MCS and will be ignored +164: [13:04:43] The provided InitialSeed is not an MCS and will be ignored +164: [13:04:43] The provided InitialSeed is not an MCS and will be ignored +164: .[13:04:43] The provided InitialSeed is not an MCS and will be ignored +164: [13:04:43] The provided InitialSeed is not an MCS and will be ignored +164: [13:04:43] The provided InitialSeed is not an MCS and will be ignored +164: .[13:04:43] The provided InitialSeed is not an MCS and will be ignored +164: [13:04:43] The provided InitialSeed is not an MCS and will be ignored +164: [13:04:43] The provided InitialSeed is not an MCS and will be ignored +164: .[13:04:43] The provided InitialSeed is not an MCS and will be ignored +164: [13:04:43] The provided InitialSeed is not an MCS and will be ignored +164: [13:04:43] The provided InitialSeed is not an MCS and will be ignored 238: ============================= test session starts ============================== 238: platform linux -- Python 3.13.7, pytest-8.3.5, pluggy-1.6.0 238: rootdir: /build/reproducible-path/rdkit-202503.1/Projects 238: configfile: pytest.ini 238: collected 12 items 238: +164: ................. +164: ---------------------------------------------------------------------- +164: Ran 60 tests in 18.072s +164: +164: OK +186: bulk +209/238 Test #164: pyFMCS ................................. Passed 19.57 sec +74: [13:04:43] Finished: testSDCorrectness() +74: [13:04:43] ----------------------------------------- +74: +210/238 Test #74: testMultithreadedMolSupplier ........... Passed 25.08 sec 234: ....... 234: ---------------------------------------------------------------------- -234: Ran 11 tests in 3.917s +234: Ran 11 tests in 6.931s 234: 234: OK -214: Enumeration has completed -214: [03:35:49] Tautomer enumeration stopped at 27 tautomers: canceled -209/238 Test #234: pySimDivPickers ........................ Passed 4.53 sec -186: [03:35:49] Relabelling existing label -183: [03:35:49] ------------------------------------- -183: [03:35:49] testing PatternHolder -173: [03:35:49] +211/238 Test #234: pySimDivPickers ........................ Passed 7.97 sec +173: [13:04:44] 173: 173: **** 173: Invariant Violation @@ -32363,1319 +33419,38 @@ 173: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitChemTransforms.so.1 173: 5# RDKit::SynthonSpaceSearch::SynthonSet::makeSynthonSearchMols() in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 173: 6# RDKit::SynthonSpaceSearch::SynthonSpace::readTextFile(std::__cxx11::basic_string, std::allocator > const&, bool&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSynthonSpaceSearch.so.1 -173: 7# 0x0000558EAF9ED90A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 8# 0x0000558EAFA3797C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 9# 0x0000558EAFA38478 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 10# 0x0000558EAFA388DA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 11# 0x0000558EAFA0A513 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 12# 0x0000558EAFA0A7FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 13# 0x0000558EAF9ECB2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch -173: 14# 0x00007F4397033CA8 in /lib/x86_64-linux-gnu/libc.so.6 +173: 7# 0x0000562D8B84090A in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 8# 0x0000562D8B88A97C in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 9# 0x0000562D8B88B478 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 10# 0x0000562D8B88B8DA in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 11# 0x0000562D8B85D513 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 12# 0x0000562D8B85D7FC in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 13# 0x0000562D8B83FB2E in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 14# 0x00007FEBA2233CA8 in /lib/x86_64-linux-gnu/libc.so.6 173: 15# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 -173: 16# 0x0000558EAF9ECB71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch +173: 16# 0x0000562D8B83FB71 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/testSynthonSpaceSubstructureSearch 173: ---------- 173: **** 173: -173: [03:35:49] Error:: in reaction amide-1 :: building molecule from synthons : 1-1 (c1cc[1*]ccc1C(=O)[1*]) and 2-1 ([1*]N1CCCC1) +173: [13:04:44] Error:: in reaction amide-1 :: building molecule from synthons : 1-1 (c1cc[1*]ccc1C(=O)[1*]) and 2-1 ([1*]N1CCCC1) 173: molzip: bond info not properly setup for bgn atom with label:1 -173: [03:35:49] Explicit valence for atom # 4 C, 5, is greater than permitted -173: [03:35:49] Error:: in reaction error-1 :: building molecule from synthons : 1-1 (C(=[2*])=CC=[1*]) and 2-1 (ClC([2*])=CN=[1*]) +173: [13:04:44] Explicit valence for atom # 4 C, 5, is greater than permitted +173: [13:04:44] Error:: in reaction error-1 :: building molecule from synthons : 1-1 (C(=[2*])=CC=[1*]) and 2-1 (ClC([2*])=CN=[1*]) 173: Explicit valence for atom # 4 C, 5, is greater than permitted -173: [03:35:49] Complex queries can be slow. -214: ..........[03:35:49] Explicit valence for atom # 1 N, 4, is greater than permitted -214: [03:35:49] Explicit valence for atom # 1 N, 4, is greater than permitted -214: [03:35:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -224: Randomness seeded to: 2173034960 +173: [13:04:44] Complex queries can be slow. +173: [13:04:44] Complex queries can be slow. +224: Randomness seeded to: 2872073620 224: =============================================================================== 224: All tests passed (203 assertions in 1 test case) 224: -210/238 Test #224: testMolProcessing ...................... Passed 5.51 sec -214: [03:35:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -173: [03:35:49] Complex queries can be slow. -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 -183: [03:35:49] ------------------------------------- -183: [03:35:49] testing TautomerPatternHolder -173: [03:35:49] Complex queries can be slow. -126: .[03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: .[03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: ..[03:35:49] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:49] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:49] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:49] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:49] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:49] DEPRECATION WARNING: please use AtomPairGenerator -126: .[03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ...[03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: [03:35:49] DEPRECATION WARNING: please use MorganGenerator -126: ....[03:35:49] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:49] DEPRECATION WARNING: please use AtomPairGenerator -126: ....[03:35:49] DEPRECATION WARNING: please use AtomPairGenerator -126: [03:35:49] DEPRECATION WARNING: please use AtomPairGenerator -126: .[03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: .[03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [03:35:49] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ... -126: ---------------------------------------------------------------------- -126: Ran 31 tests in 10.013s -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 -211/238 Test #126: pyMolDescriptors ....................... Passed 12.17 sec -173: [03:35:49] Complex queries can be slow. -183: [03:35:50] ------------------------------------- -183: [03:35:50] testSegFaultInHolder -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^[03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -186: Best mapping -183: [03:35:50] [03:35:50] SMILES Parse Error: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] [03:35:50] SMILES Parse Error: syntax errorSMILES Parse Error: syntax error while parsing: syntax error while parsing: [03:35:50] [03:35:50] [03:35:50] [03:35:50] [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdfSMILES Parse Error: [03:35:50] syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: syntax error[03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1 while parsing: SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: -183: while parsing: dsafsdf -183: -183: [03:35:50] SMILES Parse Error: check for mistakes around position :SMILES Parse Error: check for mistakes around position syntax errorsyntax error while parsing: [03:35:50] SMILES Parse Error: syntax error[03:35:50] [03:35:50] SMILES Parse Error: check for mistakes around position dsafsdf1: -183: SMILES Parse Error: -183: syntax errordsafsdf -183: 1SMILES Parse Error: :syntax error while parsing: dsafsdf -183: [03:35:50] while parsing: [03:35:50] [03:35:50] dsafsdfdsafsdf -183: [03:35:50] 1SMILES Parse Error: check for mistakes around position 1[03:35:50] -183: while parsing: : -183: SMILES Parse Error: check for mistakes around position -183: [03:35:50] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position 1: -183: 1SMILES Parse Error: check for mistakes around position -183: :[03:35:50] [03:35:50] [03:35:50] dsafsdf[03:35:50] [03:35:50] dsafsdf -183: [03:35:50] -183: dsafsdf -183: [03:35:50] [03:35:50] :dsafsdf -183: [03:35:50] ^ -183: 1dsafsdf[03:35:50] dsafsdf -183: [03:35:50] ^ -183: dsafsdf -183: -183: 1 -183: [03:35:50] [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[03:35:50] for input: '[03:35:50] SMILES Parse Error: check for mistakes around position :[03:35:50] :SMILES Parse Error: -183: ^dsafsdf[03:35:50] [03:35:50] -183: -183: dsafsdf -183: [03:35:50] dsafsdf -183: SMILES Parse Error: syntax error^ while parsing: -183: dsafsdf -183: ^[03:35:50] -183: ^ -183: [03:35:50] ' -183: -183: while parsing: 1:SMILES -183: dsafsdf -183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'Failed parsing SMILES 'dsafsdf'dsafsdf -183: for input: 'dsafsdf' -183: ^ -183: dsafsdf[03:35:50] SMILES Parse Error: syntax error while parsing: '[03:35:50] -183: ^ -183: [03:35:50] ^[03:35:50] dsafsdf -183: [03:35:50] [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[03:35:50] ' -183: -183: ^ -183: [03:35:50] SMILES Parse Error: dsafsdf -183: [03:35:50] [03:35:50] SMILESsyntax error[03:35:50] [03:35:50] [03:35:50] SMILESSMILES Parse Error: [03:35:50] [03:35:50] [03:35:50] [03:35:50] SMILES Parse Error: SMILES Parse Error: [03:35:50] while parsing: SMILES[03:35:50] SMILES Parse Error: Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf[03:35:50] -183: SMILES[03:35:50] SMILES Parse Error: check for mistakes around position Parse Error: [03:35:50] syntax errorSMILES Parse Error: check for mistakes around position while parsing: SMILES Parse Error: check for mistakes around position 1syntax error: -183: [03:35:50] dsafsdf Parse Error: Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf while parsing: -183: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[03:35:50] 1SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: for input: 'dsafsdf' -183: dsafsdf -183: ' -183: for input: 'dsafsdf' -183: Failed parsing SMILES 'dsafsdf'syntax error for input: 'dsafsdf' while parsing: dsafsdf: -183: 1SMILESFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: Parse Error: -183: [03:35:50] SMILES Parse Error: check for mistakes around position -183: dsafsdfsyntax error[03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: Failed parsing SMILES 'dsafsdf'^: while parsing: dsafsdf[03:35:50] ^ -183: [03:35:50] -183: 1 -183: dsafsdf for input: '[03:35:50] [03:35:50] SMILESSMILES Parse Error: check for mistakes around position 1: -183: Parse Error: SMILES Parse Error: check for mistakes around position :1[03:35:50] : -183: dsafsdf[03:35:50] -183: Failed parsing SMILES 'dsafsdf'[03:35:50] dsafsdf -183: [03:35:50] dsafsdfdsafsdf for input: ' -183: -183: [03:35:50] -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: ^ -183: [03:35:50] SMILES[03:35:50] [03:35:50] SMILES Parse Error: [03:35:50] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf -183: '[03:35:50] ' -183: ^dsafsdf^ -183: -183: -183: [03:35:50] Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf[03:35:50] -183: [03:35:50] SMILES Parse Error: [03:35:50] [03:35:50] ^ -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'SMILES[03:35:50] for input: '^[03:35:50] -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: SMILES Parse Error: -183: Parse Error: SMILES[03:35:50] Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'dsafsdf' -183: -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] [03:35:50] [03:35:50] syntax errorSMILESSMILES Parse Error: -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[03:35:50] for input: 'dsafsdf while parsing: Failed parsing SMILES 'dsafsdf'dsafsdfSMILES Parse Error: check for mistakes around position for input: 'dsafsdf' -183: Parse Error: -183: syntax errorFailed parsing SMILES 'dsafsdf' for input: 'dsafsdfdsafsdf'' -183: 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: -183: while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: SMILES Parse Error: check for mistakes around position 1: -183: ' -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: ' -183: dsafsdf[03:35:50] dsafsdf -183: [03:35:50] ^ -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] -183: [03:35:50] [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf[03:35:50] [03:35:50] SMILES Parse Error: check for mistakes around position [03:35:50] SMILES Parse Error: check for mistakes around position SMILES Parse Error: 1SMILES Parse Error: check for mistakes around position : -183: 1 -183: : -183: [03:35:50] dsafsdf -183: [03:35:50] 1syntax error while parsing: : -183: [03:35:50] dsafsdf -183: [03:35:50] dsafsdf^[03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: -183: -183: ^ -183: [03:35:50] [03:35:50] SMILES Parse Error: SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: syntax error while parsing: dsafsdf -183: -183: [03:35:50] [03:35:50] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: ':[03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'dsafsdf for input: 'dsafsdf' -183: ' -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf[03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position SMILES Parse Error: [03:35:50] [03:35:50] SMILES Parse Error: SMILES Parse Error: syntax error while parsing: [03:35:50] [03:35:50] SMILES Parse Error: SMILES Parse Error: [03:35:50] [03:35:50] dsafsdf -183: 1syntax error: -183: [03:35:50] dsafsdf -183: [03:35:50] ^syntax error[03:35:50] SMILES Parse Error: syntax error[03:35:50] [03:35:50] [03:35:50] SMILES Parse Error: syntax errorSMILES Parse Error: [03:35:50] syntax errordsafsdf while parsing: dsafsdf[03:35:50] syntax error -183: [03:35:50] while parsing: SMILES Parse Error: syntax error while parsing: dsafsdf -183: -183: -183: [03:35:50] SMILES Parse Error: check for mistakes around position while parsing: while parsing: dsafsdf -183: [03:35:50] [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: SMILES Parse Error: dsafsdfsyntax error[03:35:50] [03:35:50] SMILES Parse Error: check for mistakes around position SMILES Parse Error: syntax error while parsing: dsafsdf -183: 1: -183: [03:35:50] SMILES Parse Error: syntax error while parsing: [03:35:50] [03:35:50] [03:35:50] SMILES Parse Error: SMILES Parse Error: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: SMILES Parse Error: syntax error while parsing: [03:35:50] 1 while parsing: [03:35:50] dsafsdfSMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILESdsafsdf -183: -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1:SMILES Parse Error: -183: syntax error while parsing: : -183: dsafsdf[03:35:50] [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] dsafsdf -183: -183: dsafsdf -183: [03:35:50] SMILES Parse Error: [03:35:50] [03:35:50] syntax error while parsing: dsafsdf -183: [03:35:50] Parse Error: -183: SMILES Parse Error: check for mistakes around position [03:35:50] syntax error1: while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] syntax error while parsing: dsafsdf -183: [03:35:50] [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: syntax error while parsing: dsafsdf -183: [03:35:50] [03:35:50] -183: SMILES Parse Error: ^syntax error -183: dsafsdfSMILES -183: Failed parsing SMILES 'dsafsdf'[03:35:50] for input: 'dsafsdfSMILES[03:35:50] [03:35:50] [03:35:50] SMILES Parse Error: check for mistakes around position SMILES Parse Error: check for mistakes around position 1dsafsdf Parse Error: Failed parsing SMILES 'dsafsdf'[03:35:50] for input: 'dsafsdfSMILES Parse Error: 'syntax error' while parsing: [03:35:50] dsafsdf -183: SMILES Parse Error: check for mistakes around position [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: : -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: SMILES Parse Error: check for mistakes around position 1[03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position [03:35:50] SMILES Parse Error: check for mistakes around position 1:SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] [03:35:50] [03:35:50] -183: [03:35:50] [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position [03:35:50] SMILES Parse Error: ^ -183: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] [03:35:50] dsafsdf:SMILES Parse Error: syntax error -183: -183: 1:[03:35:50] while parsing: SMILES Parse Error: check for mistakes around position 1: -183: SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf^[03:35:50] SMILES Parse Error: Parse Error: SMILES Parse Error: syntax errorFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf while parsing: dsafsdf -183: -183: [03:35:50] ^[03:35:50] -183: while parsing: SMILES Parse Error: check for mistakes around position dsafsdf1 -183: :[03:35:50] SMILES Parse Error: [03:35:50] [03:35:50] SMILES Parse Error: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'syntax error[03:35:50] -183: dsafsdfdsafsdf1 -183: :SMILESdsafsdf Parse Error: -183: dsafsdf while parsing: Failed parsing SMILES 'dsafsdf'dsafsdf -183: for input: ' -183: SMILES Parse Error: check for mistakes around position dsafsdf'Failed parsing SMILES 'dsafsdf'syntax error for input: ' -183: -183: dsafsdf -183: dsafsdf' -183: -183: 1: -183: [03:35:50] while parsing: -183: [03:35:50] [03:35:50] 1 -183: [03:35:50] [03:35:50] ^dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1[03:35:50] ' -183: SMILESsyntax error[03:35:50] dsafsdf -183: [03:35:50] [03:35:50] -183: [03:35:50] SMILES -183: -183: ^ Parse Error: -183: while parsing: [03:35:50] Parse Error: [03:35:50] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfSMILES Parse Error: check for mistakes around position -183: [03:35:50] ^SMILES[03:35:50] ^ -183: [03:35:50] SMILES Parse Error: check for mistakes around position [03:35:50] ^ -183: [03:35:50] dsafsdf -183: dsafsdfSMILES Parse Error: check for mistakes around position 1SMILES Parse Error: check for mistakes around position 1 Parse Error: -183: Failed parsing SMILES 'dsafsdf'dsafsdf for input: 'Failed parsing SMILES 'dsafsdf' -183: for input: 'dsafsdfdsafsdf:SMILES Parse Error: check for mistakes around position '[03:35:50] 1[03:35:50] [03:35:50] dsafsdf -183: -183: 11: -183: [03:35:50] [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: ' -183: : -183: -183: for input: '[03:35:50] SMILES Parse Error: check for mistakes around position ^: -183: -183: dsafsdf' -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[03:35:50] dsafsdf -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: dsafsdf'[03:35:50] :[03:35:50] SMILES Parse Error: syntax error -183: while parsing: dsafsdf[03:35:50] dsafsdf -183: [03:35:50] [03:35:50] -183: 1dsafsdf -183: ^[03:35:50] : -183: -183: [03:35:50] dsafsdf -183: [03:35:50] ^[03:35:50] [03:35:50] -183: -183: [03:35:50] -183: [03:35:50] SMILES Parse Error: : -183: [03:35:50] -183: :' -183: [03:35:50] [03:35:50] dsafsdf[03:35:50] [03:35:50] syntax errordsafsdf while parsing: ^[03:35:50] SMILES^ -183: SMILES[03:35:50] SMILES -183: dsafsdfSMILES^ -183: -183: [03:35:50] Parse Error: Parse Error: -183: SMILESFailed parsing SMILES 'dsafsdf' Parse Error: Failed parsing SMILES 'dsafsdf'[03:35:50] for input: 'dsafsdfSMILES Parse Error: check for mistakes around position Failed parsing SMILES 'dsafsdf'SMILES Parse Error: for input: ' -183: ^ -183: dsafsdf -183: [03:35:50] -183: SMILES[03:35:50] for input: 'SMILESdsafsdf Parse Error: [03:35:50] Parse Error: ^[03:35:50] [03:35:50] ^ -183: [03:35:50] '1' -183: ^:SMILES -183: Failed parsing SMILES 'dsafsdf'[03:35:50] -183: [03:35:50] -183: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: ' Parse Error: dsafsdfFailed parsing SMILES 'dsafsdf'[03:35:50] for input: 'SMILESdsafsdf' -183: [03:35:50] syntax error Parse Error: [03:35:50] -183: SMILES Parse Error: SMILESdsafsdfdsafsdf -183: Failed parsing SMILES 'dsafsdf''[03:35:50] [03:35:50] SMILES Parse Error: syntax error' Parse Error: -183: Failed parsing SMILES 'dsafsdf' -183: while parsing: dsafsdf Parse Error: -183: Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: ' for input: 'dsafsdfdsafsdf' while parsing: dsafsdf -183: [03:35:50] [03:35:50] SMILES Parse Error: check for mistakes around position Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[03:35:50] [03:35:50] '^dsafsdf -183: -183: Parse Error: Failed parsing SMILES 'dsafsdf'[03:35:50] SMILES Parse Error: for input: ' for input: ' -183: dsafsdfSMILES'dsafsdf for input: 'syntax error -183: dsafsdf^'SMILES -183: ' for input: ' -183: while parsing: -183: Parse Error: 1: -183: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf Parse Error: -183: dsafsdf' -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: check for mistakes around position Failed parsing SMILES 'dsafsdf'[03:35:50] for input: 'dsafsdf1[03:35:50] :dsafsdf' -183: SMILESSMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] -183: [03:35:50] dsafsdf -183: -183: [03:35:50] ^ -183: -183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf -183: [03:35:50] [03:35:50] [03:35:50] dsafsdfSMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[03:35:50] 'dsafsdf -183: -183: [03:35:50] ^^ -183: ^ -183: -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[03:35:50] [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'SMILESdsafsdf' -183: Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[03:35:50] ^ for input: 'dsafsdf' -183: dsafsdf' -183: ' -183: -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: SMILES Parse Error: check for mistakes around position [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: 1: -183: dsafsdf -183: [03:35:50] ^ -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] SMILES Parse Error: syntax error while parsing: dsafsdf -183: [03:35:50] SMILES Parse Error: check for mistakes around position 1: -183: [03:35:50] dsafsdf -183: [03:35:50] ^ -183: [03:35:50] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -183: [03:35:50] ------------------------------------- -183: [03:35:50] Results do not depend on numThreads -173: [03:35:50] Complex queries can be slow. -212/238 Test #186: testRGroupDecomp ....................... Passed 9.02 sec -173: [03:35:50] Complex queries can be slow. -209: CN=c1cc[nH]cn1 -209: CN=c1ccnc[nH]1 -209: CNc1ccncn1 -209: res: CNc1ccncn1 -209: CN=c1cccc[nH]1 -209: CNc1ccccn1 -209: res: CNc1ccccn1 -173: [03:35:50] Complex queries can be slow. -173: [03:35:50] Complex queries can be slow. -213/238 Test #209: molTautomerTest ........................ Passed 7.65 sec -173: [03:35:51] Complex queries can be slow. -29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -74: [03:35:51] Finished: testSmiCorrectness() -74: [03:35:51] ----------------------------------------- -74: -74: [03:35:51] -74: ----------------------------------------- -74: [03:35:51] Spurious data before the first property will be ignored -74: [03:35:51] Property will be truncated after the first blank line -74: [03:35:51] Property will be truncated after the first blank line -74: [03:35:51] Property will be truncated after the first blank line -214: ............[03:35:51] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:35:51] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -214: [03:35:51] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -159: Done -159: ----------------- Test Github #781: Rendering single-atom molecules -173: [03:35:51] Complex queries can be slow. -159: Done -159: ----------------- Test 3 -29: All 191 tests passed -159: file test3_1.png gave hash 123800385U not the expected 675908852U -170: Randomness seeded to: 2461797206 -170: [03:35:51] Timed out after 11 seconds. -159: file test3_2.png gave hash 1032419673U not the expected 2452584093U -159: file test3_3.png gave hash 4020047355U not the expected 1907006999U -159: file test3_4.png gave hash 3725504342U not the expected 2305641511U -159: file test3_5.png gave hash 3317652686U not the expected 3842605920U -159: file test3_6.png gave hash 513359294U not the expected 662622011U -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -159: file test3_7.png gave hash 98439579U not the expected 469729412U -159: Done -159: ----------------- Test Github774: upside-down drawings -159: file test774_1.png gave hash 2947517748U not the expected 428322245U -159: file test774_2.png gave hash 3968995771U 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 1401513420U not the expected 271517011U -159: file test852_2.png gave hash 1268186246U 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 2465667142U not the expected 2835587240U -173: [03:35:51] Complex queries can be slow. -159: file test860_2.png gave hash 3702727304U not the expected 1116015475U -159: file test860_3.png gave hash 524479710U 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 -214: ........[03:35:51] Explicit valence for atom # 1 O, 3, is greater than permitted -159: Done -159: ----------------- Testing drawMolecules -159: file test12_1.svg gave hash 76786371U not the expected 826649652U -74: [03:35:51] Finished: testSDCorrectness() -74: [03:35:51] ----------------------------------------- -74: -214/238 Test #74: testMultithreadedMolSupplier ........... Passed 14.51 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 -214: .. -214: ---------------------------------------------------------------------- -214: Ran 38 tests in 8.047s -214: -214: OK -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. -214: done -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. -215/238 Test #214: pyMolStandardize ....................... Passed 8.42 sec -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 1197378089U not the expected 200877868U -159: file test20_2.png gave hash 717262667U not the expected 1651164846U -159: file test20_3.png gave hash 1844565424U not the expected 1463603076U -159: file test20_4.png gave hash 284908271U 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 3066881557U not the expected 3303791649U -159: file testGithub3305_2.png gave hash 3473051322U not the expected 4003267433U -159: file testGithub3305_3.png gave hash 748608900U not the expected 273338209U -159: file testGithub3305_4.png gave hash 3317652686U not the expected 3842605920U -159: file testGithub3305_5.png gave hash 2008868897U not the expected 151279576U -159: file testGithub3305_5.svg gave hash 3310590632U not the expected 1335449325U -159: file testGithub3305_6.png gave hash 1479310253U not the expected 613418460U -159: file testGithub3305_7.png gave hash 526001191U 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 -216/238 Test #159: moldraw2DTest1 ......................... Passed 12.23 sec -217/238 Test #201: pyTestThreads .......................... Passed 9.64 sec +173: [13:04:44] Complex queries can be slow. +212/238 Test #224: testMolProcessing ...................... Passed 9.42 sec +173: [13:04:45] Complex queries can be slow. +150: processing +150: launch :0 +150: launch :1 +150: launch :2 +150: launch :3 177: VS001: PASSED 177: VS002: PASSED 177: VS003: PASSED @@ -33978,31 +33753,260 @@ 177: VS300: PASSED 177: Check finished: 0 molecules failed. 177: Failed: -218/238 Test #177: pyCIPLabelsValidation .................. Passed 12.63 sec -152: .............[03:35:53] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:35:53] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:35:53] Molecule does not have explicit Hs. Consider calling AddHs() -80: =============================================================================== -80: All tests passed (1596 assertions in 100 test cases) -80: -152: [03:35:53] Molecule does not have explicit Hs. Consider calling AddHs() -219/238 Test #80: fileParsersCatchTest ................... Passed 16.50 sec -152: [03:35:53] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:35:53] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:35:53] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:35:53] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:35:53] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:35:53] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:35:53] Molecule does not have explicit Hs. Consider calling AddHs() -183: [03:35:53] ------------------------------------- -183: [03:35:53] Results do not depend on numThreads (all same) -183: [03:35:54] ------------------------------------- -183: [03:35:54] testTautomerQueries -183: [03:35:54] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -183: [03:35:54] ------------------------------------- -183: [03:35:54] github3881 recursive smarts with rings -220/238 Test #183: substructLibraryTest ................... Passed 13.12 sec -197: ..[03:35:54] +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 +213/238 Test #201: pyTestThreads .......................... Passed 12.74 sec +126: Warning: Atom Count for residue ARG64A does not match expected count +126: Warning: Atom Count for residue LYS80A does not match expected count +214/238 Test #177: pyCIPLabelsValidation .................. Passed 20.35 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: .[13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: .[13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: ..[13:04:45] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:45] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:45] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:45] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:45] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:45] DEPRECATION WARNING: please use AtomPairGenerator +126: .[13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +173: [13:04:45] Complex queries can be slow. +126: [13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ...[13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: [13:04:45] DEPRECATION WARNING: please use MorganGenerator +126: ....[13:04:45] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:45] DEPRECATION WARNING: please use AtomPairGenerator +126: ....[13:04:45] DEPRECATION WARNING: please use AtomPairGenerator +126: [13:04:45] DEPRECATION WARNING: please use AtomPairGenerator +126: .[13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [13:04:45] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ... +126: ---------------------------------------------------------------------- +126: Ran 31 tests in 22.185s +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 +215/238 Test #126: pyMolDescriptors ....................... Passed 25.99 sec +173: [13:04:46] Complex queries can be slow. +186: bulk, no symmetry +214: Enumeration has completed +214: [13:04:46] Tautomer enumeration stopped at 17 tautomers: canceled +173: [13:04:46] Complex queries can be slow. +173: [13:04:49] Complex queries can be slow. +214: ..........[13:04:50] Explicit valence for atom # 1 N, 4, is greater than permitted +214: [13:04:50] Explicit valence for atom # 1 N, 4, is greater than permitted +214: [13:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [13:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +173: [13:04:50] Complex queries can be slow. +186: [13:04:51] Relabelling existing label +173: [13:04:51] Complex queries can be slow. +173: [13:04:52] Complex queries can be slow. +186: Best mapping +216/238 Test #186: testRGroupDecomp ....................... Passed 25.34 sec +214: ............[13:04:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [13:04:53] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +214: [13:04:53] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +159: Done +159: ----------------- Test Github #781: Rendering single-atom molecules +159: Done +159: ----------------- Test 3 +159: file test3_1.png gave hash 123800385U not the expected 675908852U +159: file test3_2.png gave hash 1032419673U not the expected 2452584093U +159: file test3_3.png gave hash 4020047355U not the expected 1907006999U +159: file test3_4.png gave hash 3725504342U not the expected 2305641511U +159: file test3_5.png gave hash 3317652686U not the expected 3842605920U +159: file test3_6.png gave hash 513359294U not the expected 662622011U +214: ........[13:04:53] Explicit valence for atom # 1 O, 3, is greater than permitted +159: file test3_7.png gave hash 98439579U not the expected 469729412U +159: Done +159: ----------------- Test Github774: upside-down drawings +159: file test774_1.png gave hash 2947517748U not the expected 428322245U +159: file test774_2.png gave hash 3968995771U 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 1401513420U not the expected 271517011U +159: file test852_2.png gave hash 1268186246U 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 2465667142U not the expected 2835587240U +159: file test860_2.png gave hash 3702727304U not the expected 1116015475U +183: [13:04:54] ------------------------------------- +183: [13:04:54] Results do not depend on numThreads (all same) +159: file test860_3.png gave hash 524479710U not the expected 1872467868U +159: Done +159: ----------------- Test Github #910: ugly coordinates generated for peptide chains +183: [13:04:54] ------------------------------------- +183: [13:04:54] testTautomerQueries +214: .. +214: ---------------------------------------------------------------------- +214: Ran 38 tests in 18.786s +214: +214: OK +214: done +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 +183: [13:04:54] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +159: ----------------- Testing drawing a second molecule +183: [13:04:54] ------------------------------------- +183: [13:04:54] github3881 recursive smarts with rings +159: Done +159: ----------------- Testing drawing a grid of molecules +217/238 Test #183: substructLibraryTest ................... Passed 28.25 sec +159: Done +159: ----------------- Testing drawMolecules +159: file test12_1.svg gave hash 76786371U not the expected 826649652U +218/238 Test #214: pyMolStandardize ....................... Passed 20.26 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. +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 1197378089U not the expected 200877868U +159: file test20_2.png gave hash 717262667U not the expected 1651164846U +159: file test20_3.png gave hash 1844565424U not the expected 1463603076U +159: file test20_4.png gave hash 284908271U 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 3066881557U not the expected 3303791649U +159: file testGithub3305_2.png gave hash 3473051322U not the expected 4003267433U +159: file testGithub3305_3.png gave hash 748608900U not the expected 273338209U +159: file testGithub3305_4.png gave hash 3317652686U not the expected 3842605920U +159: file testGithub3305_5.png gave hash 2008868897U not the expected 151279576U +159: file testGithub3305_5.svg gave hash 3310590632U not the expected 1335449325U +159: file testGithub3305_6.png gave hash 1479310253U not the expected 613418460U +197: ..[13:04:55] 197: 197: **** 197: Pre-condition Violation @@ -34016,7 +34020,7 @@ 197: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C0F75062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F3EF36E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34027,17 +34031,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F9C0CDB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x00007F9C0CDB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x00007F9C0CDB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x00007F9C0CDB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x00007F9C0CDB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007F3EF0DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x00007F3EF0DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x00007F3EF0DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x00007F3EF0DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x00007F3EF0DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x00007F9C0F74D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x00007F3EF36E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x00000000005CBA19 in /usr/bin/python3 @@ -34069,13 +34073,13 @@ 197: 55# 0x00000000006B339E in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x00007F9C0FF38CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 58# 0x00007F3EF3ECFCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [03:35:54] +197: [13:04:55] 197: 197: **** 197: Pre-condition Violation @@ -34089,7 +34093,7 @@ 197: 2# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C0F75062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F3EF36E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34100,17 +34104,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F9C0CDB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x00007F9C0CDB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x00007F9C0CDB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x00007F9C0CDB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x00007F9C0CDB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007F3EF0DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x00007F3EF0DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x00007F3EF0DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x00007F3EF0DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x00007F3EF0DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x00007F9C0F74D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x00007F3EF36E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x00000000005CBA19 in /usr/bin/python3 @@ -34142,13 +34146,13 @@ 197: 55# 0x00000000006B339E in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x00007F9C0FF38CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 58# 0x00007F3EF3ECFCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [03:35:54] +197: [13:04:55] 197: 197: **** 197: Pre-condition Violation @@ -34162,7 +34166,7 @@ 197: 2# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C0F75062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F3EF36E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34173,17 +34177,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F9C0CDB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x00007F9C0CDB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x00007F9C0CDB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x00007F9C0CDB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x00007F9C0CDB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007F3EF0DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x00007F3EF0DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x00007F3EF0DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x00007F3EF0DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x00007F3EF0DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x00007F9C0F74D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x00007F3EF36E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x00000000005CBA19 in /usr/bin/python3 @@ -34215,13 +34219,13 @@ 197: 55# 0x00000000006B339E in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x00007F9C0FF38CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 58# 0x00007F3EF3ECFCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [03:35:54] +197: [13:04:55] 197: 197: **** 197: Pre-condition Violation @@ -34235,7 +34239,7 @@ 197: 2# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C0F75062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F3EF36E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34246,17 +34250,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F9C0CDB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x00007F9C0CDB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x00007F9C0CDB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x00007F9C0CDB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x00007F9C0CDB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007F3EF0DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x00007F3EF0DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x00007F3EF0DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x00007F3EF0DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x00007F3EF0DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x00007F9C0F74D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x00007F3EF36E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x00000000005CBA19 in /usr/bin/python3 @@ -34288,15 +34292,18 @@ 197: 55# 0x00000000006B339E in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x00007F9C0FF38CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 58# 0x00007F3EF3ECFCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: [03:35:54] +197: [13:04:55] 197: 197: **** +159: file testGithub3305_7.png gave hash 526001191U not the expected 2835747678U +159: Done +159: ----------------- Test Github 3391 - maxFontSize interacting badly with DrawMolecules. 197: Pre-condition Violation 197: no owner 197: Violation occurred on line 153 in file ./Code/GraphMol/Atom.h @@ -34308,7 +34315,7 @@ 197: 2# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C0F75062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F3EF36E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34319,17 +34326,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F9C0CDB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x00007F9C0CDB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x00007F9C0CDB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x00007F9C0CDB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x00007F9C0CDB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007F3EF0DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x00007F3EF0DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x00007F3EF0DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x00007F3EF0DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x00007F3EF0DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x00007F9C0F74D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x00007F3EF36E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x00000000005CBA19 in /usr/bin/python3 @@ -34361,13 +34368,13 @@ 197: 55# 0x00000000006B339E in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x00007F9C0FF38CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 58# 0x00007F3EF3ECFCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: .....[03:35:54] +197: .....[13:04:55] 197: 197: **** 197: Range Error @@ -34381,7 +34388,7 @@ 197: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C0F75062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F3EF36E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34392,17 +34399,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F9C0CDB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x00007F9C0CDB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x00007F9C0CDB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x00007F9C0CDB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x00007F9C0CDB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007F3EF0DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x00007F3EF0DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x00007F3EF0DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x00007F3EF0DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x00007F3EF0DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x00007F9C0F74D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x00007F3EF36E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x00000000005CBA19 in /usr/bin/python3 @@ -34434,57 +34441,57 @@ 197: 55# 0x00000000006B339E in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x00007F9C0FF38CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 58# 0x00007F3EF3ECFCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: ......[03:35:54] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -197: [03:35:54] ERROR: Smiles parse error on line 0 -197: [03:35:54] ERROR: Cannot create molecule from : 'c1ccccc' -197: [03:35:54] SMILES Parse Error: extra open parentheses while parsing: C(C -197: [03:35:54] SMILES Parse Error: check for mistakes around position 2: -197: [03:35:54] C(C -197: [03:35:54] ~^ -197: [03:35:54] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -197: [03:35:54] ERROR: Smiles parse error on line 3 -197: [03:35:54] ERROR: Cannot create molecule from : 'C(C' -197: [03:35:54] Explicit valence for atom # 1 C, 5, is greater than permitted -197: [03:35:54] ERROR: Could not sanitize molecule on line 6 -197: [03:35:54] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -197: [03:35:54] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -197: [03:35:54] ERROR: Smiles parse error on line 0 -197: [03:35:54] ERROR: Cannot create molecule from : 'c1ccccc' -197: [03:35:54] SMILES Parse Error: extra open parentheses while parsing: C(C -197: [03:35:54] SMILES Parse Error: check for mistakes around position 2: -197: [03:35:54] C(C -197: [03:35:54] ~^ -197: [03:35:54] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -197: [03:35:54] ERROR: Smiles parse error on line 3 -197: [03:35:54] ERROR: Cannot create molecule from : 'C(C' -197: [03:35:54] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -197: [03:35:54] ERROR: Smiles parse error on line 6 -197: [03:35:54] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -197: [03:35:54] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [03:35:54] ERROR: Could not sanitize molecule ending on line 21 -197: [03:35:54] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -197: [03:35:54] ERROR: EOF hit while reading atoms -197: [03:35:54] ERROR: moving to the beginning of the next molecule -197: [03:35:54] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [03:35:54] ERROR: Could not sanitize molecule ending on line 21 -197: [03:35:54] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -197: [03:35:54] ERROR: EOF hit while reading atoms -197: [03:35:54] ERROR: moving to the beginning of the next molecule -95: 0,0 0 -95: 0,1 0 -95: 1,0 0 -95: 1,1 0 -95: 2,0 0 -95: 2,1 0 -197: ....[03:35:54] +159: Done +159: ----------------- Test Github 4156 - bad scale for radicals in grid +197: ......[13:04:55] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +197: [13:04:55] ERROR: Smiles parse error on line 0 +197: [13:04:55] ERROR: Cannot create molecule from : 'c1ccccc' +197: [13:04:55] SMILES Parse Error: extra open parentheses while parsing: C(C +197: [13:04:55] SMILES Parse Error: check for mistakes around position 2: +197: [13:04:55] C(C +197: [13:04:55] ~^ +197: [13:04:55] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +197: [13:04:55] ERROR: Smiles parse error on line 3 +197: [13:04:55] ERROR: Cannot create molecule from : 'C(C' +197: [13:04:55] Explicit valence for atom # 1 C, 5, is greater than permitted +197: [13:04:55] ERROR: Could not sanitize molecule on line 6 +197: [13:04:55] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +197: [13:04:55] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +197: [13:04:55] ERROR: Smiles parse error on line 0 +197: [13:04:55] ERROR: Cannot create molecule from : 'c1ccccc' +197: [13:04:55] SMILES Parse Error: extra open parentheses while parsing: C(C +197: [13:04:55] SMILES Parse Error: check for mistakes around position 2: +197: [13:04:55] C(C +197: [13:04:55] ~^ +197: [13:04:55] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +197: [13:04:55] ERROR: Smiles parse error on line 3 +197: [13:04:55] ERROR: Cannot create molecule from : 'C(C' +197: [13:04:55] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +197: [13:04:55] ERROR: Smiles parse error on line 6 +197: [13:04:55] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +197: [13:04:55] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [13:04:55] ERROR: Could not sanitize molecule ending on line 21 +197: [13:04:55] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +197: [13:04:55] ERROR: EOF hit while reading atoms +197: [13:04:55] ERROR: moving to the beginning of the next molecule +197: [13:04:55] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [13:04:55] ERROR: Could not sanitize molecule ending on line 21 +197: [13:04:55] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +197: [13:04:55] ERROR: EOF hit while reading atoms +197: [13:04:55] ERROR: moving to the beginning of the next molecule +159: Done +159: ----------------- Test JSON atomColourPalette +197: ....[13:04:55] 197: 197: **** +159: Done +159: ----------------- Test draw aromatic OR queries 197: Pre-condition Violation 197: RingInfo not initialized 197: Violation occurred on line 170 in file ./Code/GraphMol/RingInfo.cpp @@ -34496,7 +34503,7 @@ 197: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 197: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C0F75062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F3EF36E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34507,17 +34514,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F9C0CDB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x00007F9C0CDB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x00007F9C0CDB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x00007F9C0CDB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x00007F9C0CDB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007F3EF0DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x00007F3EF0DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x00007F3EF0DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x00007F3EF0DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x00007F3EF0DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x00007F9C0F74D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x00007F3EF36E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x00000000005CBA19 in /usr/bin/python3 @@ -34549,14 +34556,17 @@ 197: 55# 0x00000000006B339E in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x00007F9C0FF38CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 58# 0x00007F3EF3ECFCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -221/238 Test #95: testEnumeration ........................ Passed 17.02 sec -197: .............[03:35:54] +159: Done +159: ----------------- Test AND queries +159: Done +219/238 Test #159: moldraw2DTest1 ......................... Passed 31.75 sec +197: .............[13:04:55] 197: 197: **** 197: Range Error @@ -34570,7 +34580,7 @@ 197: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 197: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 5# 0x00007F9C0F75062C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 5# 0x00007F3EF36E762C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdSLNParse.so 197: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34581,17 +34591,17 @@ 197: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 197: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 197: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 16# 0x00007F9C0CDB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 17# 0x00007F9C0CDB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 18# 0x00007F9C0CDB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 19# 0x00007F9C0CDB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -197: 20# 0x00007F9C0CDB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 16# 0x00007F3EF0DB79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 17# 0x00007F3EF0DB79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 18# 0x00007F3EF0DB7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 19# 0x00007F3EF0DB7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +197: 20# 0x00007F3EF0DB7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 197: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 197: 25# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -197: 26# 0x00007F9C0F74D3C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +197: 26# 0x00007F3EF36E43C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 197: 27# _PyObject_MakeTpCall in /usr/bin/python3 197: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 197: 29# 0x00000000005CBA19 in /usr/bin/python3 @@ -34623,70 +34633,125 @@ 197: 55# 0x00000000006B339E in /usr/bin/python3 197: 56# Py_RunMain in /usr/bin/python3 197: 57# Py_BytesMain in /usr/bin/python3 -197: 58# 0x00007F9C0FF38CA8 in /lib/x86_64-linux-gnu/libc.so.6 +197: 58# 0x00007F3EF3ECFCA8 in /lib/x86_64-linux-gnu/libc.so.6 197: 59# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 197: 60# _start in /usr/bin/python3 197: ---------- 197: **** 197: -197: ...[03:35:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -197: ............................[03:35:55] SMILES Parse Error: unclosed ring for input: 'C1CC' +197: ...[13:04:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +29: Checking against /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +29: All 191 tests passed +197: ............................[13:04:56] SMILES Parse Error: unclosed ring for input: 'C1CC' 197: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8| -197: 643 -197: ..[03:35:55] WARNING: not removing hydrogen atom without neighbors -197: [03:35:55] WARNING: not removing hydrogen atom with dummy atom neighbors -197: [03:35:55] WARNING: not removing hydrogen atom with wedged bond -197: [03:35:55] WARNING: not removing hydrogen atom without neighbors -197: [03:35:55] WARNING: not removing hydrogen atom with dummy atom neighbors -197: ......[03:35:56] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [03:35:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 -197: .[03:35:56] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [03:35:56] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [03:35:56] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [03:35:56] Explicit valence for atom # 1 F, 2, is greater than permitted -197: [03:35:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 -197: [03:35:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 -197: [03:35:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 -197: ..........[03:35:56] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -197: [03:35:56] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -197: .[03:35:56] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -197: [03:35:56] SMILES Parse Error: check for mistakes around position 4: -197: [03:35:56] CCC |$foo;;bar$| ourname -197: [03:35:56] ~~~^ -197: [03:35:56] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -197: ..[03:35:56] SMILES Parse Error: syntax error while parsing: error -197: [03:35:56] SMILES Parse Error: check for mistakes around position 1: -197: [03:35:56] error -197: [03:35:56] ^ -197: [03:35:56] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -197: [03:35:56] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -197: [03:35:56] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -197: [03:35:56] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -197: .........................[03:35:56] SMILES Parse Error: syntax error while parsing: garbage_0 -197: [03:35:56] SMILES Parse Error: check for mistakes around position 1: -197: [03:35:56] garbage_0 -197: [03:35:56] ^ -197: [03:35:56] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -197: [03:35:56] SMILES Parse Error: syntax error while parsing: garbage_2 -197: [03:35:56] SMILES Parse Error: check for mistakes around position 1: -197: [03:35:56] garbage_2 -197: [03:35:56] ^ -197: [03:35:56] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -197: [03:35:56] SMILES Parse Error: syntax error while parsing: garbage_4 -197: [03:35:56] SMILES Parse Error: check for mistakes around position 1: -197: [03:35:56] garbage_4 -197: [03:35:56] ^ -197: [03:35:56] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +197: 1 +197: ..[13:04:56] WARNING: not removing hydrogen atom without neighbors +197: [13:04:56] WARNING: not removing hydrogen atom with dummy atom neighbors +197: [13:04:56] WARNING: not removing hydrogen atom with wedged bond +197: [13:04:56] WARNING: not removing hydrogen atom without neighbors +197: [13:04:56] WARNING: not removing hydrogen atom with dummy atom neighbors +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202503.1/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... +197: ......[13:04:59] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [13:04:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 +197: .[13:04:59] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [13:04:59] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [13:04:59] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [13:04:59] Explicit valence for atom # 1 F, 2, is greater than permitted +197: [13:04:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 +197: [13:04:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 +197: [13:04:59] Can't kekulize mol. Unkekulized atoms: 0 1 2 +197: ..........[13:04:59] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +197: [13:04:59] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +197: .[13:04:59] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +197: [13:04:59] SMILES Parse Error: check for mistakes around position 4: +197: [13:04:59] CCC |$foo;;bar$| ourname +197: [13:04:59] ~~~^ +197: [13:04:59] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +197: ..[13:04:59] SMILES Parse Error: syntax error while parsing: error +197: [13:04:59] SMILES Parse Error: check for mistakes around position 1: +197: [13:04:59] error +197: [13:04:59] ^ +197: [13:04:59] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +197: [13:04:59] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +197: [13:04:59] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +197: [13:04:59] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +197: .........................[13:04:59] SMILES Parse Error: syntax error while parsing: garbage_0 +197: [13:04:59] SMILES Parse Error: check for mistakes around position 1: +197: [13:04:59] garbage_0 +197: [13:04:59] ^ +197: [13:04:59] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +197: [13:04:59] SMILES Parse Error: syntax error while parsing: garbage_2 +197: [13:04:59] SMILES Parse Error: check for mistakes around position 1: +197: [13:04:59] garbage_2 +197: [13:04:59] ^ +197: [13:04:59] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +197: [13:04:59] SMILES Parse Error: syntax error while parsing: garbage_4 +197: [13:04:59] SMILES Parse Error: check for mistakes around position 1: +197: [13:04:59] garbage_4 +197: [13:04:59] ^ +197: [13:04:59] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' 197: ............ 197: ---------------------------------------------------------------------- -197: Ran 279 tests in 13.066s +197: Ran 279 tests in 26.428s 197: 197: OK 197: supplier: 197: supplier: 197: supplier: -222/238 Test #197: pyGraphMolWrap ......................... Passed 13.93 sec -185: ......[03:35:56] +220/238 Test #197: pyGraphMolWrap ......................... Passed 27.77 sec +80: =============================================================================== +80: All tests passed (1596 assertions in 100 test cases) +80: +221/238 Test #80: fileParsersCatchTest ................... Passed 41.59 sec +152: .............[13:05:03] Molecule does not have explicit Hs. Consider calling AddHs() +152: [13:05:03] Molecule does not have explicit Hs. Consider calling AddHs() +152: [13:05:03] Molecule does not have explicit Hs. Consider calling AddHs() +152: [13:05:03] Molecule does not have explicit Hs. Consider calling AddHs() +152: [13:05:03] Molecule does not have explicit Hs. Consider calling AddHs() +152: [13:05:03] Molecule does not have explicit Hs. Consider calling AddHs() +152: [13:05:03] Molecule does not have explicit Hs. Consider calling AddHs() +152: [13:05:03] Molecule does not have explicit Hs. Consider calling AddHs() +152: [13:05:03] Molecule does not have explicit Hs. Consider calling AddHs() +152: [13:05:03] Molecule does not have explicit Hs. Consider calling AddHs() +152: [13:05:03] Molecule does not have explicit Hs. Consider calling AddHs() +95: 0,0 0 +95: 0,1 0 +95: 1,0 0 +95: 1,1 0 +95: 2,0 0 +95: 2,1 0 +222/238 Test #95: testEnumeration ........................ Passed 50.03 sec +152: ...[13:05:13] Molecule does not have explicit Hs. Consider calling AddHs() +152: [13:05:13] Molecule does not have explicit Hs. Consider calling AddHs() +152: [13:05:13] Molecule does not have explicit Hs. Consider calling AddHs() +152: [13:05:13] Molecule does not have explicit Hs. Consider calling AddHs() +152: [13:05:13] Molecule does not have explicit Hs. Consider calling AddHs() +152: ... +152: ---------------------------------------------------------------------- +152: Ran 19 tests in 48.280s +152: +152: OK +152: Testing MolAlign Wrappers +223/238 Test #152: pyMolAlign ............................. Passed 49.77 sec +29: Checking against /build/reproducible-path/rdkit-202503.1/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 +224/238 Test #29: testMMFFForceField ..................... Passed 57.86 sec +185: ......[13:05:18] 185: 185: **** 185: Pre-condition Violation @@ -34707,25 +34772,25 @@ 185: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 185: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 12# 0x00007F46B285D195 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 12# 0x00007FB43125D195 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 14# 0x00007F46B4CB662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 14# 0x00007FB43367562C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 185: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 185: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 185: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 20# 0x00007F46B27B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 21# 0x00007F46B27B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x00007F46B27B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x00007F46B27B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x00007F46B27B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 20# 0x00007FB4311B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 21# 0x00007FB4311B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x00007FB4311B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x00007FB4311B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x00007FB4311B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 29# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 30# 0x00007F46B4CB33C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 30# 0x00007FB4336723C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 31# _PyObject_MakeTpCall in /usr/bin/python3 185: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 33# 0x00000000005CBA19 in /usr/bin/python3 @@ -34757,13 +34822,13 @@ 185: 59# 0x00000000006B339E in /usr/bin/python3 185: 60# Py_RunMain in /usr/bin/python3 185: 61# Py_BytesMain in /usr/bin/python3 -185: 62# 0x00007F46B55FFCA8 in /lib/x86_64-linux-gnu/libc.so.6 +185: 62# 0x00007FB433FBECA8 in /lib/x86_64-linux-gnu/libc.so.6 185: 63# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 185: 64# _start in /usr/bin/python3 185: ---------- 185: **** 185: -185: [03:35:56] +185: [13:05:18] 185: 185: **** 185: Pre-condition Violation @@ -34775,7 +34840,7 @@ 185: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 185: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitRDGeneral.so.1 185: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 -185: 3# 0x00007F46B22E66C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 +185: 3# 0x00007FB430CE66C0 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 185: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitGraphMol.so.1 185: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 185: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 @@ -34785,25 +34850,25 @@ 185: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu//lib/libRDKitSubstructMatch.so.1 185: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 13# 0x00007F46B285D195 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 13# 0x00007FB43125D195 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 15# 0x00007F46B4CB662C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 15# 0x00007FB43367562C in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 185: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdmolfiles.so 185: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 185: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 21# 0x00007F46B27B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 22# 0x00007F46B27B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 23# 0x00007F46B27B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 24# 0x00007F46B27B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so -185: 25# 0x00007F46B27B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 21# 0x00007FB4311B79F3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 22# 0x00007FB4311B79C3 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 23# 0x00007FB4311B7993 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 24# 0x00007FB4311B7963 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so +185: 25# 0x00007FB4311B7933 in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so 185: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu/rdkit/rdBase.so 185: 30# boost::python::handle_exception_impl(boost::function0) in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 -185: 31# 0x00007F46B4CB33C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 +185: 31# 0x00007FB4336723C6 in /lib/x86_64-linux-gnu/libboost_python313.so.1.83.0 185: 32# _PyObject_MakeTpCall in /usr/bin/python3 185: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 185: 34# 0x00000000005CBA19 in /usr/bin/python3 @@ -34835,73 +34900,38 @@ 185: 60# 0x00000000006B339E in /usr/bin/python3 185: 61# Py_RunMain in /usr/bin/python3 185: 62# Py_BytesMain in /usr/bin/python3 -185: 63# 0x00007F46B55FFCA8 in /lib/x86_64-linux-gnu/libc.so.6 +185: 63# 0x00007FB433FBECA8 in /lib/x86_64-linux-gnu/libc.so.6 185: 64# __libc_start_main in /lib/x86_64-linux-gnu/libc.so.6 185: 65# _start in /usr/bin/python3 185: ---------- 185: **** 185: -152: ...[03:35:56] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:35:56] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:35:56] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:35:56] Molecule does not have explicit Hs. Consider calling AddHs() -152: [03:35:56] Molecule does not have explicit Hs. Consider calling AddHs() -152: ... -152: ---------------------------------------------------------------------- -152: Ran 19 tests in 16.885s -152: -152: OK -152: Testing MolAlign Wrappers -223/238 Test #152: pyMolAlign ............................. Passed 17.21 sec -29: Checking against /build/reproducible-path/rdkit-202503.1/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 -224/238 Test #29: testMMFFForceField ..................... Passed 20.64 sec -185: ............. -185: ---------------------------------------------------------------------- -185: Ran 19 tests in 17.521s -185: -185: OK -185: Testing atom rings -185: testing bond rings -185: searching atom rings -185: searching bond rings -185: done -225/238 Test #185: pySubstructLibrary ..................... Passed 18.30 sec -173: [03:36:00] Complex queries can be slow. -173: [03:36:00] Complex queries can be slow. +173: [13:05:20] Complex queries can be slow. +51: Randomness seeded to: 1790249137 +51: =============================================================================== +51: All tests passed (14835 assertions in 14 test cases) +51: +225/238 Test #51: canonTestsCatch ........................ Passed 62.11 sec +173: [13:05:20] Complex queries can be slow. +173: [13:05:20] Complex queries can be slow. +173: [13:05:21] Complex queries can be slow. +173: [13:05:21] Complex queries can be slow. +173: [13:05:22] Complex queries can be slow. +173: [13:05:22] Complex queries can be slow. +173: [13:05:23] Complex queries can be slow. +173: [13:05:24] Complex queries can be slow. +173: [13:05:25] Complex queries can be slow. 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -163: TOTAL Time elapsed 20.28 seconds -226/238 Test #163: testFMCS ............................... Passed 20.34 sec -173: [03:36:00] Complex queries can be slow. -51: Randomness seeded to: 650857502 -51: =============================================================================== -51: All tests passed (14835 assertions in 14 test cases) -51: -227/238 Test #51: canonTestsCatch ........................ Passed 23.32 sec -173: [03:36:00] Complex queries can be slow. -173: [03:36:00] Complex queries can be slow. -173: [03:36:00] Complex queries can be slow. -173: [03:36:00] Complex queries can be slow. -173: [03:36:01] Complex queries can be slow. +163: TOTAL Time elapsed 61.48 seconds +173: [13:05:25] Complex queries can be slow. +226/238 Test #163: testFMCS ............................... Passed 61.66 sec +173: [13:05:26] Complex queries can be slow. +173: [13:05:26] Complex queries can be slow. 150: --------------------------------- 150: test O3A multithreading bug 150: @@ -34909,67 +34939,65 @@ 150: testCrippenO3A multithreading 150: 150: generating reference data -173: [03:36:01] Complex queries can be slow. -173: [03:36:01] Complex queries can be slow. +148: .........[13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +148: [13:05:27] Molecule does not have explicit Hs. Consider calling AddHs() +173: [13:05:27] Complex queries can be slow. +173: [13:05:27] Complex queries can be slow. 150: processing 150: launch :0 150: launch :1 150: launch :2 150: launch :3 -173: [03:36:01] Complex queries can be slow. -173: [03:36:01] Complex queries can be slow. -173: [03:36:02] Complex queries can be slow. -148: .........[03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -148: [03:36:02] Molecule does not have explicit Hs. Consider calling AddHs() -173: [03:36:02] Complex queries can be slow. -173: [03:36:02] Complex queries can be slow. -173: [03:36:02] Complex queries can be slow. -173: [03:36:02] Complex queries can be slow. -173: [03:36:03] Complex queries can be slow. -212: [03:36:04] Explicit valence for atom # 0 Br, 1, is greater than permitted -212: =============================================================================== -212: All tests passed (38344 assertions in 51 test cases) -212: -228/238 Test #212: molStandardizeCatchTest ................ Passed 20.94 sec -173: [03:36:04] Complex queries can be slow. +173: [13:05:28] Complex queries can be slow. +173: [13:05:28] Complex queries can be slow. +173: [13:05:29] Complex queries can be slow. +173: [13:05:29] Complex queries can be slow. 173: =============================================================================== 173: All tests passed (121 assertions in 17 test cases) 173: -229/238 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 24.08 sec +227/238 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 65.38 sec 148: ... 148: ---------------------------------------------------------------------- -148: Ran 22 tests in 26.047s +148: Ran 22 tests in 73.906s 148: 148: OK -230/238 Test #148: pyDistGeomHelpers ...................... Passed 26.66 sec -5: [03:36:10] Finished: testMultipleTimes() -5: [03:36:10] -5: ----------------------------------------- -231/238 Test #5: testConcurrentQueue .................... Passed 33.47 sec -150: --------------------------------- -150: test getO3AForProbeConfs -150: -150: *********************************************************** -232/238 Test #150: testO3AAlign ........................... Passed 31.75 sec +228/238 Test #148: pyDistGeomHelpers ...................... Passed 75.29 sec +212: [13:05:45] Explicit valence for atom # 0 Br, 1, is greater than permitted +212: =============================================================================== +212: All tests passed (38344 assertions in 51 test cases) +212: +229/238 Test #212: molStandardizeCatchTest ................ Passed 71.67 sec +170: [13:05:47] Timed out after 71 seconds. +185: ............. +185: ---------------------------------------------------------------------- +185: Ran 19 tests in 80.258s +185: +185: OK +185: Testing atom rings +185: testing bond rings +185: searching atom rings +185: searching bond rings +185: done +230/238 Test #185: pySubstructLibrary ..................... Passed 81.97 sec 238: DbCLI/UnitTestDbCLI.py ............ [100%] 238: 238: =============================== warnings summary =============================== @@ -34978,30 +35006,31 @@ 238: decBase = declarative_base() 238: 238: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -238: ======================== 12 passed, 1 warning in 27.32s ======================== -233/238 Test #238: pythonProjectTests ..................... Passed 27.92 sec -147: [03:36:16] UFFTYPER: Unrecognized atom type: S_6+6 (0) -147: [03:36:16] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -147: [03:36:16] UFFTYPER: Unrecognized charge state for atom: 0 -146: [03:36:28] done -146: [03:36:28] --------------------------------- -146: [03:36:28] test github issue 256: handling of zero-atom molecules +238: =================== 12 passed, 1 warning in 76.67s (0:01:16) =================== +231/238 Test #238: pythonProjectTests ..................... Passed 78.59 sec +150: --------------------------------- +150: test getO3AForProbeConfs +150: +150: *********************************************************** +232/238 Test #150: testO3AAlign ........................... Passed 99.66 sec +147: [13:06:09] UFFTYPER: Unrecognized atom type: S_6+6 (0) +147: [13:06:09] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +147: [13:06:09] UFFTYPER: Unrecognized charge state for atom: 0 +146: [13:06:47] done +146: [13:06:47] --------------------------------- +146: [13:06:47] test github issue 256: handling of zero-atom molecules 146: -146: [03:36:28] --------------------------------- -146: [03:36:28] test embedder callback function -146: [03:36:28] --------------------------------- -146: [03:36:28] test multi-threaded multi-conf embedding +146: [13:06:47] --------------------------------- +146: [13:06:47] test embedder callback function +146: [13:06:47] --------------------------------- +146: [13:06:47] test multi-threaded multi-conf embedding 146: -146: [03:36:30] --------------------------------- -146: [03:36:30] test github issue 563: Incorrect ring stereochemistry after embedding +146: [13:06:58] --------------------------------- +146: [13:06:58] 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: -234/238 Test #171: testRascalCluster ...................... Passed 50.80 sec -146: [03:36:32] --------------------------------- -146: [03:36:32] test github issue 568: Incorrect stereochemistry after embedding +146: [13:07:01] --------------------------------- +146: [13:07:01] 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 @@ -35015,19 +35044,20 @@ 146: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O 146: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 146: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 +170: =============================================================================== +170: All tests passed (3590 assertions in 35 test cases) +170: +233/238 Test #170: testRascalMCES ......................... Passed 172.55 sec 146: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 146: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 146: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 +171: =============================================================================== +171: All tests passed (93 assertions in 5 test cases) +171: +234/238 Test #171: testRascalCluster ...................... Passed 176.36 sec 146: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O 146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O -146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O -146: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 -170: =============================================================================== -170: All tests passed (3590 assertions in 35 test cases) -170: -235/238 Test #170: testRascalMCES ......................... Passed 65.70 sec -146: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 -147: [03:36:48] Interrupted, cancelling conformer generation +147: [13:07:24] 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] @@ -35060,11 +35090,14 @@ 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: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 +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: -236/238 Test #147: distGeomHelpersCatch ................... Passed 69.45 sec +235/238 Test #147: distGeomHelpersCatch ................... Passed 182.52 sec +146: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 +146: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 +146: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 146: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 146: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 146: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 @@ -35072,48 +35105,52 @@ 146: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 146: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 146: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] -146: [03:37:02] Molecule does not have explicit Hs. Consider calling AddHs() -146: [03:36:57] --------------------------------- -146: [03:36:57] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system -146: [03:36:57] --------------------------------- -146: [03:36:57] More ChEMBL molecules failing bounds smoothing. -146: [03:36:57] --------------------------------- -146: [03:36:57] ugly conformations can be generated for highly constrained ring systems. -146: [03:36:57] --------------------------------- -146: [03:36:57] test embed parameters structure. -146: [03:36:57] --------------------------------- -146: [03:36:57] test github 1227: Hs being used in RMSD filtering. -146: [03:36:57] --------------------------------- -146: [03:36:57] Failure to embed larger aromatic rings. -146: [03:36:59] --------------------------------- -146: [03:36:59] Deterministic with large random seeds -146: [03:37:01] --------------------------------- -146: [03:37:01] Github #1990: seg fault after RemoveHs -146: [03:37:01] --------------------------------- -146: [03:37:01] Github #2246: Use coordMap when starting embedding from random coords -146: [03:37:02] --------------------------------- -146: [03:37:02] Providing a distance bounds matrix. -146: [03:37:02] --------------------------------- -146: [03:37:02] Disabling fragmentation. -146: [03:37:02] --------------------------------- -146: [03:37:02] Using symmetry in conformation pruning. -146: [03:37:02] --------------------------------- -146: [03:37:02] Force trans amides. -146: [03:37:02] --------------------------------- -146: [03:37:02] test missing Hs warning. -146: [03:37:02] --------------------------------- -146: [03:37:02] basic H bond support. -146: [03:37:02] ******************************************************* -237/238 Test #146: testDistGeomHelpers .................... Passed 82.75 sec -174: Randomness seeded to: 934471878 +146: [13:08:06] Molecule does not have explicit Hs. Consider calling AddHs() +146: [13:07:46] --------------------------------- +146: [13:07:46] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system +146: [13:07:46] --------------------------------- +146: [13:07:46] More ChEMBL molecules failing bounds smoothing. +146: [13:07:46] --------------------------------- +146: [13:07:46] ugly conformations can be generated for highly constrained ring systems. +146: [13:07:46] --------------------------------- +146: [13:07:46] test embed parameters structure. +146: [13:07:47] --------------------------------- +146: [13:07:47] test github 1227: Hs being used in RMSD filtering. +146: [13:07:49] --------------------------------- +146: [13:07:49] Failure to embed larger aromatic rings. +146: [13:07:54] --------------------------------- +146: [13:07:54] Deterministic with large random seeds +146: [13:08:02] --------------------------------- +146: [13:08:02] Github #1990: seg fault after RemoveHs +146: [13:08:03] --------------------------------- +146: [13:08:03] Github #2246: Use coordMap when starting embedding from random coords +146: [13:08:06] --------------------------------- +146: [13:08:06] Providing a distance bounds matrix. +146: [13:08:06] --------------------------------- +146: [13:08:06] Disabling fragmentation. +146: [13:08:06] --------------------------------- +146: [13:08:06] Using symmetry in conformation pruning. +146: [13:08:06] --------------------------------- +146: [13:08:06] Force trans amides. +146: [13:08:06] --------------------------------- +146: [13:08:06] test missing Hs warning. +146: [13:08:06] --------------------------------- +146: [13:08:06] basic H bond support. +146: [13:08:06] ******************************************************* +236/238 Test #146: testDistGeomHelpers .................... Passed 223.33 sec +174: Randomness seeded to: 2327016980 174: =============================================================================== 174: All tests passed (28 assertions in 2 test cases) 174: -238/238 Test #174: testSynthonSpaceRascalSearch ........... Passed 104.74 sec +237/238 Test #174: testSynthonSpaceRascalSearch ........... Passed 327.51 sec +5: [13:11:21] Finished: testMultipleTimes() +5: [13:11:21] +5: ----------------------------------------- +238/238 Test #5: testConcurrentQueue .................... Passed 423.36 sec 100% tests passed, 0 tests failed out of 238 -Total Test time (real) = 108.10 sec +Total Test time (real) = 423.54 sec make[2]: Leaving directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' create-stamp debian/debhelper-build-stamp @@ -35123,7 +35160,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202503.1' dh_auto_install - cd obj-x86_64-linux-gnu && make -j40 install DESTDIR=/build/reproducible-path/rdkit-202503.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/rdkit-202503.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202503.1 -B/build/reproducible-path/rdkit-202503.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -35134,1278 +35171,1278 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDRandom.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemutils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemdraw_qax.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/retest.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/listutils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/cactvs.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemdraw.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/cactvs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/listutils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/retest.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemdraw_qax.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/fileutils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/chemutils.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/spiral.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/utils/fileutils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DistanceGeometry/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/TestRunner.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Geometry +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Geometry/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Randomize.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/LazyGenerator.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/SigFactory.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/Generate.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/Utils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm2D/Matcher.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatFinderCLI.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fraggle +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fraggle/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fraggle/FraggleSim.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EnumerateHeterocycles.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/BuildFragmentCatalog.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SimpleEnum +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SimpleEnum/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SimpleEnum/Enumerator.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ReducedGraphs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SATIS.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/PandasTools.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/AtomTypes.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/EState.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/EState_VSA.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EState/Fingerprinter.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemicalFeatures.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/PyMol.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SpacialScore.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/EnumerateStereoisomers.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Scaffolds +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Scaffolds/ScaffoldNetwork.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Scaffolds/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Scaffolds/MurckoScaffold.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/PandasPatcher.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/QED.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Suppliers +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Suppliers/MolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Suppliers/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Suppliers/DbMolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Torsions.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Sheridan.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Utils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AtomPairs/Pairs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/BRICS.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/TorsionFingerprints.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FilterCatalog.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/GraphDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Crippen.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Lipinski.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMapParser.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMapPoint.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMapUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FeatMaps/FeatMaps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemicalForceFields.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FragmentMatcher.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/PropertyMol.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FunctionalGroups.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/RegistrationHash.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests/ChEMBL_quinolones.tsv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests/rdkit-structure-renderer.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/nbtests/github4823.ipynb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolStandardize +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolStandardize/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolCatalog.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Descriptors3D.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ShowMols.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/BuilderUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeObjects.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/demoCombined.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeBuilder.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeAligner.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/MolSimilarity.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/SimilarityScreener.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/ClusterMols.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/DbFpSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fingerprints/FingerprintMols.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/TemplateAlign.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/TemplateExpand.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/SDFToCSV.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/DescriptorUtilities.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/BulkTester.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemUtils/AlignDepict.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features/ShowFeats.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features/FeatDirUtilsRD.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Features/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/DSViewer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FragmentCatalog.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MACCSkeys.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FastSDMolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/fmcs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/fmcs/fmcs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AllChem.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/ExcludedVolume.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/EmbedLib.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Pharm3D/Pharmacophore.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MCS.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey/InchiInfo.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey/MolKey.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolKey/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Graphs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolSurf.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SaltRemover.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Fragments.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/IPythonConsole.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/MolDrawing.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/FreeSans.ttf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/SimilarityMaps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Draw/InteractiveRenderer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Descriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Recap.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/inchi.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/FingerprintUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader_sa.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/MolDb/Loader_orig.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Stats.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/MLData.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/DataUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/SplitData.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Transforms.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/FindQuantBounds.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Quantize.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/files.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/Risk.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/Scoring.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/CompoundDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/Parser.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/Descriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/entropy.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitRank.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitClusterer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/VoteImg.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MatOps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterVis.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/murtagh_test.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Clusters.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Resemblance.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Murtagh.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Standardize.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Butina.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt4.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/Fontmapping.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/pidPyart.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/pidSVG.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/colors.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/stringformat.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pagesizes.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pidPDF.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgen.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgeom.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfgen.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfdoc.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfmetrics.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pidPDF.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfutils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PDF/pdfmetrics.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/pidReportLab.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/HTMLPiddler.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/psmetrics.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/fontinfo.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/latin1MetricsCache.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/pidPS.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pid.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/pidtest.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/pstests.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/testallps.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/tests/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/pidSVG.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/SVG/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/pidPyart.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/Fontmapping.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Pyart/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/utils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/stringformat.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/colors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pidPIL.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pidPIL.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pid.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/HTMLPiddler.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/util/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWxDc.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWX.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/pagesizes.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/Qt/pidQt4.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/formatted-strings.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/TK/pidTK.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/ReportLab/pidReportLab.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/utils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/psmetrics.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/pidPS.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/fontinfo.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/PS/latin1MetricsCache.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWX.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/WX/pidWxDc.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/sping/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Numerics/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/HierarchyVis.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/VectCollection.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/TopNContainer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/LazySignature.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitUtils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsemble.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsembleDb.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Avalon -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Avalon/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/pytest.ini -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Output.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Node.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Supply.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Transform.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Supply.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Node.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SDSupply.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesSupply.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesSupply.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/demo.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/DbMolSupply.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SDSupply.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/VLib/Output.py -- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Subshape/SubshapeBuilder.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/BRICS.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/FastSDMolSupplier.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/ChemicalFeatures.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/SpacialScore.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/AllChem.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/Chem/Crippen.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ForceField/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/VectCollection.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitUtils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/LazySignature.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/TopNContainer.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsembleDb.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/HierarchyVis.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/DataStructs/BitEnsemble.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDRandom.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/TestRunner.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Murtagh.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterUtils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Butina.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/ClusterVis.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Standardize.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/murtagh_test.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Resemblance.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Cluster/Clusters.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MLUtils/VoteImg.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/MatOps.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Scoring/Scoring.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/Risk.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/SLT/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitRank.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/BitClusterer.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/InfoTheory/entropy.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/files.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/Descriptors.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/CompoundDescriptors.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Descriptors/Parser.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Transforms.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Quantize.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/FindQuantBounds.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/SplitData.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/MLData.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/DataUtils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/ML/Data/Stats.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/RDLogger.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/conftest.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/SimilarityPickers.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/python3.13/site-packages/rdkit/SimDivFilters/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/rddata.sql --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/RDData.sqlt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Salts.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Crippen.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/RDData.sqlt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/README.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/README.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/rddata.sql +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Salts.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Data/Crippen.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo.inkscape.svg --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo.lrg.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/wiki --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Images/logo.ai +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png +-- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/index.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/introduction_jp.rst -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png --- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_20.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_19.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_44.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png --- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_59.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_15.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_28.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_35.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_61.png +-- Installing: 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Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_18.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_60.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_42.png +-- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_29.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_51.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_16.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_6.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_36.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png +-- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_15_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_29_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_6.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mfp2_bit872.svg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_7.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/rdkit_fork_clone.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/pull_req1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1_highlight.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_representation2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553_2.svg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_35_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_6.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im6.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/query_atoms.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example5.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/ary_group.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im5.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_15_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_39_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molA.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_example4.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_3_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/Cc1ccccc1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im2.svg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/stereo_annotation.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molB.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im0.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.jpg +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molG.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_5.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_12.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/mol_metadata1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molD.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im4.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im4.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp3.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im5.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molC.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im2.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im1.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_5.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Docs/Book/images/atrop_representation1.png -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/mol_transform.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/indexing.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/rfrag.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/create_mmp_db.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/search_mmp_db.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans_smarts.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxratio.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_fragmented.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks_mol_trans.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_smi.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mol_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smiles_mol_trans.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_default.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs_smarts.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_smi_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_transfroms.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_smart_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_smarts_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_output.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_rfrag.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/MolVS --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/MolVS/molvs_cli.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/README.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/ChiralDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/utils.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/README.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/__init__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/identifyReactants.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/efgs -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/efgs/efgs.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/efgs/README.md --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/efgs/try_efgs.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/efgs/ch33query.sql --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/setup.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/requirements.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/pytest.ini --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/README.md --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test/test_freewilson.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_scaffold.mol --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_act.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/freewilson.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/efgs/try_efgs.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CMakeLists.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/M_Kossner -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/Frames.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/README --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/fraggle.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/rdkit_tversky.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/atomcontrib.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/readme.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/final_fraggle_results.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query_fragmentation.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/ChEMBL_11265_actives.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/fragmentation_tversky_out --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/cxn_tversky.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fastcluster.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered.tsv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/sdf2smi.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/cdk2.sdf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/cdk2.smi --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/build_sascore_db.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/FilterSet_NIBR2019_wPubChemExamples.html +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/README.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/SubstructureFilter_HitTriaging_wPubChemExamples.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/filterExamples.png +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100_out.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i23_1C9.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3w2c_N15.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/BEG_test.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/JVE_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/AKI_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i24_1C9.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/lig_crystal_aligned.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dpv.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1C9_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dt0.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/N15_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/6c83.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3m11_AKI.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/README.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/BEG.png +-- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score/publicnp.model.gz +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score/npscorer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/testData -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/README -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/pbf.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/PBF/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/MolVS +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/MolVS/molvs_cli.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/IFG/README +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/build_sascore_db.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score/npscorer.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score/publicnp.model.gz --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/README.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/identifyReactants.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/utils.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/Examples_CalcLigRMSD.ipynb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/README.md --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/1C9.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/AKI.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/N15.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/5dpv_complex.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/BEG.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/JVE.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/6c83_complex.png --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i24_1C9.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3m11_AKI.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i23_1C9.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dpv.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/6c83.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/AKI_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/BEG_test.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/lig_crystal_aligned.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/JVE_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_1.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1C9_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dt0.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/N15_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3w2c_N15.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/README.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/ChiralDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/atomcontrib.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query.smi +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/final_fraggle_results.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/fragmentation_tversky_out +-- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fastcluster.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered.tsv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/cdk2.smi +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_rfrag.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/mmpa/data +-- Installing: 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/build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/rdConformerParser.cpp --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/CMakeLists.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/SubstructureFilter_HitTriaging_wPubChemExamples.csv --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/README.md --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/FilterSet_NIBR2019_wPubChemExamples.html --- Installing: 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Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.h +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.cpp +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/requirements.txt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810.smi +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_act.csv +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_scaffold.mol +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/README.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test/test_freewilson.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/pytest.ini +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/freewilson.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/setup.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/.gitignore -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/README.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/.gitignore -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/CACHEDIR.TAG -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache/stepwise -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/.pytest_cache/v/cache/nodeids --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/pytest.ini -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr_q1.mol -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.smi +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.2.smi -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/pubchem.200.sdf +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr_q1.mol -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Fingerprints.sqlt +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/loadErrors.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Compounds.sqlt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Descriptors.sqlt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/loadErrors.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/AtomPairs.sqlt --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/README -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.sdf --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.2.smi +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/README -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__ -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__/CreateDb.cpython-313.pyc -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__/UnitTestDbCLI.cpython-313-pytest-8.3.5.pyc -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/__pycache__/SearchDb.cpython-313.pyc +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/SearchDb.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/CreateDb.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/moe_like.dsc -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/UnitTestDbCLI.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/SearchDb.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/DbCLI/moe_like.dsc +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Projects/pytest.ini -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/create_deb_packages.sh --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/PythonFormat.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/FeatFinderCLI.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/test.sh -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/README.md +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/create_deb_packages.sh -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/clang_worker.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/__main__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/FeatFinderCLI.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/clang_worker.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/patch_rdkit_docstrings/__init__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/__main__.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/worker.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/__init__.py --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/gen_rdkit_stubs/__main__.py +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/Scripts/PythonFormat.py -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/README.md -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/share/RDKit/license.txt -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDInchiLib.so.1.2025.03.1 @@ -36451,12 +36488,12 @@ -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/BetterEnums.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/enum.h -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash +-- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash_fwd.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/extensions.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/hash_float.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/float_functions.hpp --- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDBoost.so.1.2025.03.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDBoost.so.1 -- Installing: /build/reproducible-path/rdkit-202503.1/debian/tmp/usr/lib/libRDKitRDBoost.so @@ -37083,10 +37120,7 @@ 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 rdAlignment.so to rdAlignment.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 rdSimDivPickers.so to rdSimDivPickers.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 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 @@ -37132,11 +37166,14 @@ 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 rdForceField.so to rdForceField.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 Clustering.so to Clustering.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 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 Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. make[1]: Leaving directory '/build/reproducible-path/rdkit-202503.1' @@ -37763,45 +37800,45 @@ dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake +dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol pg_detoast_datum: it's probably a plugin +dpkg-shlibdeps: warning: 24 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 -dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol palloc0: it's probably a plugin -dpkg-shlibdeps: warning: 24 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 -dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2025.03.1 found in none of the libraries dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake -dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: 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: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202503.1-5_amd64.deb'. -dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202503.1-5_all.deb'. -dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202503.1-5_amd64.deb'. dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202503.1-5_amd64.deb'. -dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202503.1-5_amd64.deb'. -dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202503.1-5_amd64.deb'. -dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202503.1-5_amd64.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202503.1-5_amd64.deb'. +dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202503.1-5_amd64.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202503.1-5_all.deb'. +dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202503.1-5_amd64.deb'. +dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202503.1-5_all.deb'. +dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202503.1-5_amd64.deb'. +dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202503.1-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202503.1-5_amd64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202503.1-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -37809,12 +37846,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1070101/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1070101/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/988309 and its subdirectories -I: Current time: Tue Sep 9 03:43:57 -12 2025 -I: pbuilder-time-stamp: 1757432637 +I: removing directory /srv/workspace/pbuilder/1070101 and its subdirectories +I: Current time: Tue Oct 13 13:23:34 +14 2026 +I: pbuilder-time-stamp: 1791847414