Diff of the two buildlogs: -- --- b1/build.log 2024-11-05 13:16:19.358749289 +0000 +++ b2/build.log 2024-11-05 14:20:22.022090313 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Dec 8 07:22:02 -12 2025 -I: pbuilder-time-stamp: 1765221722 +I: Current time: Wed Nov 6 03:16:26 +14 2024 +I: pbuilder-time-stamp: 1730812586 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -34,52 +34,84 @@ dpkg-source: info: applying pg16 I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3055525/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1159142/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 5 13:17 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1159142/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1159142/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='844c266ba2184b74888b3a1693936e66' - 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='3055525' - PS1='# ' - PS2='> ' + INVOCATION_ID=7351eacb647d4273a53d63323a31b805 + 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=1159142 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.0LBcgZNT/pbuilderrc_kGTZ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0LBcgZNT/b1 --logfile b1/build.log rdkit_202309.3-7.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0LBcgZNT/pbuilderrc_u8eE --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0LBcgZNT/b2 --logfile b2/build.log rdkit_202309.3-7.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos5-amd64 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3055525/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1159142/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -552,7 +584,7 @@ Get: 358 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2024.20241102-1 [8757 kB] Get: 359 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2024.20241102-1 [17.0 MB] Get: 360 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2024.20241102-1 [24.6 MB] -Fetched 413 MB in 9s (43.7 MB/s) +Fetched 413 MB in 20s (21.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19968 files and directories currently installed.) @@ -1711,8 +1743,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Dec 8 19:24:53 UTC 2025. -Universal Time is now: Mon Dec 8 19:24:53 UTC 2025. +Local time is now: Tue Nov 5 13:21:03 UTC 2024. +Universal Time is now: Tue Nov 5 13:21:03 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-3.2) ... @@ -2094,7 +2126,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202309.3/ && 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_202309.3-7_source.changes +I: user script /srv/workspace/pbuilder/1159142/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1159142/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202309.3/ && 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_202309.3-7_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202309.3-7 dpkg-buildpackage: info: source distribution unstable @@ -2293,8 +2329,8 @@ This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find Boost (missing: program_options) (found suitable version "1.83.0", minimum required is "1.58.0") --- Configuring done (1.5s) --- Generating done (1.2s) +-- Configuring done (8.6s) +-- Generating done (8.4s) CMake Warning: Manually-specified variables were not used by the project: @@ -2313,7 +2349,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_auto_build - cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202309.3 -B/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -2321,114 +2357,114 @@ make[3]: Entering directory '/build/reproducible-path/rdkit-202309.3/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 -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend -make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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-202309.3/Code/ML/Cluster/Murtagh/hc.c [ 3%] Linking C shared library ../../../../lib/libRDKithc.so cd 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2023.09.3 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 3%] Built target hc -[ 3%] Linking CXX shared library ../../lib/libRDKitga.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2023.09.3 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o CMakeFiles/ga.dir/util/Util.cpp.o /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so [ 3%] Linking CXX static library librdkitCatch.a cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake cd 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2023.09.3 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 3%] Built target ga [ 3%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2023.09.3 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so @@ -2443,456 +2479,378 @@ [ 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 -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake "--color=" +make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake "--color=" +make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseBitVect.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build +[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o +cd 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/DiscreteDistMat.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DiscreteDistMat.cpp [ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -[ 6%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -[ 6%] Building CXX object 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseBitVect.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202309.3/Code/DataStructs/DiscreteValueVect.cpp [ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o -[ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS 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-c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/FPBReader.cpp +[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/MultiFPBReader.cpp [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Catalogs/CatalogEntry.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS 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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/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DiscreteDistMat.cpp -[ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -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_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-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/DistPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/DistPicker.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS 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-c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/FPBReader.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -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_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-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202309.3/Code/SimDivPickers/MaxMinPicker.cpp +[ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -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_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-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202309.3/Code/SimDivPickers/HierarchicalClusterPicker.cpp [ 6%] Linking CXX executable testMatCalc cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 6%] Linking CXX executable testConcurrentQueue +cd 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../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so +[ 6%] Linking CXX shared library ../../lib/libRDKitCatalogs.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 6%] Built target EigenSolvers +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2023.09.3 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so 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/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2023.09.3 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 7%] Linking CXX executable testConcurrentQueue -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConcurrentQueue.dir/link.txt --verbose=1 cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2023.09.3 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -o testConcurrentQueue ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 7%] Built target SimDivPickers -[ 7%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202309.3/Code/SimDivPickers/testPickers.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 7%] Built target testConcurrentQueue -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 7%] Built target EigenSolvers -[ 7%] Linking CXX executable logTestsCatch -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 7%] Built target logTestsCatch -[ 7%] Linking CXX shared library ../../lib/libRDKitCatalogs.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2023.09.3 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 7%] Built target Catalogs [ 7%] Linking CXX executable testMatrices cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 7%] Built target testMatrices -[ 7%] Linking CXX executable testQuery -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 7%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 +[ 7%] Linking CXX executable dictTestsCatch +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2023.09.3 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 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 7%] Built target testQuery +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/libCatch2.a /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 7%] Built target DataStructs make -f 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f 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/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform3D.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202309.3/Code/DataStructs/testFPB.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK 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-c /build/reproducible-path/rdkit-202309.3/Code/Geometry/UniformGrid3D.cpp [ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o [ 8%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -[ 8%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -[ 8%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202309.3/Code/SimDivPickers/catch_tests.cpp +[ 8%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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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/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-202309.3/Code/DataStructs/testDatastructs.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform3D.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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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/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform2D.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/UniformGrid3D.cpp +[ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/GridUtils.cpp -[ 9%] Linking CXX executable testSimDivPickers -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2023.09.3 ../../lib/libRDKithc.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so 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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/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/AlignPoints.cpp +[ 12%] Linking CXX executable testDict +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o -MF CMakeFiles/testGrid.dir/testGrid.cpp.o.d -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/testGrid.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/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-202309.3/Code/Geometry/catch_tests.cpp -[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o -[ 14%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o -[ 14%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -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 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Bond.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o -MF CMakeFiles/testGrid.dir/testGrid.cpp.o.d -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/testGrid.cpp /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:190:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' 190 | python::def("BulkDiceSimilarity", &BulkDice>, @@ -3153,177 +3111,255 @@ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::boost::python::converter::extract_rvalue >.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -[ 16%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -MF CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp -[ 16%] Linking CXX executable testFPB +[ 14%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202309.3/Code/Geometry/catch_tests.cpp +[ 14%] Linking CXX executable testFPB cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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/usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -[ 16%] Built target testFPB -make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend +[ 14%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 +[ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o +cd 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202309.3/Code/Geometry/Wrap/Point.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 16%] Built target Clustering -[ 16%] Linking CXX shared library ../../../lib/libRDKitAlignment.so +[ 14%] Built target rdMetricMatrixCalc +make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make 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Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/testConrec.cpp +[ 14%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2023.09.3 CMakeFiles/Alignment.dir/AlignPoints.cpp.o 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/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 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Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-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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testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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--verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testConrec.dir/testConrec.cpp.o -o testConrec ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 19%] Built target testChemicalFeatures -[ 20%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o ../../../../lib/libRDKitInfoTheory.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so 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Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-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-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/ROMol.cpp.o -MF CMakeFiles/GraphMol.dir/ROMol.cpp.o.d -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.cpp +[ 16%] Linking CXX executable testDataStructs cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-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-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -MF CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o.d -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.cpp +[ 17%] Built target testChemicalFeatures +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/atomic_data.cpp +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/QueryOps.cpp.o -MF CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.cpp +[ 17%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindRings.cpp:1348:36: warning: unused parameter 'mol' [-Wunused-parameter] + 1348 | void findRingFamilies(const ROMol &mol) { + | ~~~~~~~~~~~~~^~~ /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 17%] Built target rdAlignment +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Aromaticity.cpp +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -MF CMakeFiles/GraphMol.dir/Kekulize.cpp.o.d -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Kekulize.cpp +[ 19%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 +[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/ConjugHybrid.cpp.o -MF CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o.d -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ConjugHybrid.cpp +/usr/bin/c++ -fPIC 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -MF CMakeFiles/GraphMol.dir/RingInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RingInfo.cpp +[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.cpp +[ 19%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-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/rdGeometry.cpp.o 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -MF CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o.d -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AdjustQuery.cpp +[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Resonance.cpp +[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/StereoGroup.cpp.o -MF CMakeFiles/GraphMol.dir/StereoGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StereoGroup.cpp +[ 20%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-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/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.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -MF CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/new_canon.cpp +[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/SubstanceGroup.cpp.o -MF CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstanceGroup.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 21%] Built target cDataStructs +[ 20%] Built target cDataStructs +[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FindStereo.cpp.o -MF 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/NontetrahedralStereo.cpp.o -MF CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/NontetrahedralStereo.cpp +[ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/WedgeBonds.cpp.o -MF CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o.d -o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/WedgeBonds.cpp [ 21%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2023.09.3 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o CMakeFiles/GraphMol.dir/Resonance.cpp.o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o CMakeFiles/GraphMol.dir/new_canon.cpp.o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o CMakeFiles/GraphMol.dir/FindStereo.cpp.o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl @@ -3340,931 +3376,940 @@ make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make[4]: Entering directory 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"--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.cpp -[ 22%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGenericGroups_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERICGROUPS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Rule4c.cpp.o -MF 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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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/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-202309.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp -[ 25%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so +[ 22%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so cd 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Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Node.cpp.o -MF CMakeFiles/CIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Node.cpp +[ 23%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2023.09.3 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2023.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so -[ 25%] Built target PartialCharges +[ 23%] Built target Trajectory make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake "--color=" +[ 23%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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-fPIC -MD -MT Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp -[ 25%] Built target MolCatalog -make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -MF CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o.d -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp -[ 26%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so -cd 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CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 26%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2023.09.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2023.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 26%] Built target Trajectory -make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend -[ 26%] Built target CIPLabeler +[ 23%] Built target MolCatalog make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu' -[ 26%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Edge.cpp.o -MF CMakeFiles/CIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Edge.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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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/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/LinearSearch.cpp +[ 25%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Wrap/rdTrajectory.cpp +[ 25%] Built target MolTransforms +make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/PositionConstraint.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS 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-c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.cpp -[ 31%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so +[ 26%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. 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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/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-202309.3/Code/GraphMol/SLNParse/SLNAttribs.cpp +[ 26%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 31%] Built target GenericGroups +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +[ 26%] Built target GenericGroups make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct 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&& /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Substruct/SubstructMatch.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Substruct/SubstructUtils.cpp -[ 32%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp +[ 26%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2023.09.3 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 32%] Built target MolTransforms +[ 26%] Built target Optimizer make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp +[ 26%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/SLNParse/sln.tab.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp +[ 27%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../../lib/libRDKitChemicalFeatures.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 27%] Built target rdChemicalFeatures +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 33%] Built target rdPartialCharges -[ 34%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2023.09.3 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.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202309.3/Code/ForceField/UFF/BondStretch.cpp +[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-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/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202309.3/Code/ForceField/UFF/TorsionAngle.cpp +[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/DistanceConstraint.cpp +[ 31%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 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/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.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o +cd 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-std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleConstraint.cpp +[ 31%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 31%] Built target SmilesParse +make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 31%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionConstraint.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../lib/libRDKitMolInterchange.so.1 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-std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/PositionConstraint.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 34%] Built target rdtrajectory -[ 34%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so +make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 32%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202309.3/Code/GraphMol/itertest.cpp +[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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/Params.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Params.cpp +[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleBend.cpp +[ 33%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 34%] Built target ShapeHelpers -make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend +[ 33%] Built target ShapeHelpers +make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 34%] Built target rdMolCatalog +make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 34%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -MF CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o.d -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/test-valgrind.cpp +[ 34%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o CMakeFiles/CIPLabeler.dir/Node.cpp.o CMakeFiles/CIPLabeler.dir/Edge.cpp.o CMakeFiles/CIPLabeler.dir/Sort.cpp.o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so [ 34%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-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.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 34%] Built target rdqueries -[ 34%] Linking CXX shared library ../../lib/libRDKitForceField.so -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2023.09.3 CMakeFiles/ForceField.dir/ForceField.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/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/Params.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/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 34%] Built target ForceField -[ 34%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 34%] Built target MolInterchange -make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend +[ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/OopBend.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so 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/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionAngle.cpp +[ 34%] Built target CIPLabeler +make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build +make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 34%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp -[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 34%] Built target rdSLNParse -[ 34%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 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../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so +[ 34%] Building CXX object Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -MF CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o.d -o CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_queries.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 34%] 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/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.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-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake "--color=" +[ 34%] Built target rdqueries make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color=" +[ 34%] Building CXX object Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202309.3/Code/GraphMol/catch_molbundle.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 +[ 34%] Built target rdMolTransforms 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-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make 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/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake "--color=" +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend +[ 34%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202309.3/Code/GraphMol/SmilesParse/test2.cpp +[ 35%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2023.09.3 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build -make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o -MF CMakeFiles/testSubgraphs1.dir/test1.cpp.o.d -o CMakeFiles/testSubgraphs1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/test1.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2023.09.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so +[ 35%] Building CXX object 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-g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 36%] Built target rdMolTransforms +[ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionConstraint.cpp +[ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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-o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/PositionConstraint.cpp [ 36%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o 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-std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 36%] Built target SubstructMatch -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend -make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend -make[4]: Entering directory 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'/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/DependInfo.cmake "--color=" +[ 36%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -o queryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 43%] Built target graphmolIterTest -[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp -[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 +[ 41%] Built target molbundleTestsCatch +make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintUtil.cpp -[ 43%] Linking CXX executable graphmolcpTest -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 41%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -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_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Filters.cpp.o -MF CMakeFiles/FilterCatalog.dir/Filters.cpp.o.d -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Filters.cpp +[ 41%] Linking CXX executable testSubgraphs1 +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp +[ 41%] Built target testSubgraphs1 +make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 43%] Built target graphmolcpTest -[ 44%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK 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../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS 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CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Fingerprints.cpp +[ 41%] Linking CXX shared library ../../lib/libRDKitForceField.so +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2023.09.3 CMakeFiles/ForceField.dir/ForceField.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/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/Params.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/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 44%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp -[ 44%] Linking CXX executable moliteratorTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 -[ 44%] Built target testSubgraphs2 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -o moliteratorTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 41%] Built target ForceField +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 44%] Built target moliteratorTestsCatch -[ 44%] Linking CXX executable molbundleTestsCatch -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -o molbundleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/PatternFingerprints.cpp +[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 44%] Built target molbundleTestsCatch -[ 44%] Linking CXX executable testSubgraphs1 -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 41%] Built target rdCIPLabeler +[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp +[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp +[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so +cd 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../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 41%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong 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cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp -[ 44%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 41%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION 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Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp +[ 42%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MACCS.cpp.o -MF CMakeFiles/Fingerprints.dir/MACCS.cpp.o.d -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MACCS.cpp +[ 42%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2023.09.3 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 43%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so -[ 44%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2023.09.3 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 44%] Built target MolAlign +[ 43%] Built target MolAlign +[ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ 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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-202309.3/Code/GraphMol/Fingerprints/MHFP.cpp +[ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FingerprintGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp +[ 44%] Linking CXX executable testReducedGraphs +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 44%] Built target rdReducedGraphs +[ 44%] Linking CXX executable graphmolqueryTest +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 +[ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp +[ 44%] Linking CXX executable testSLNParse +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E 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CMakeFiles/Depictor.dir/Templates.cpp.o.d -o CMakeFiles/Depictor.dir/Templates.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Templates.cpp [ 44%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -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-202309.3/Code/DistGeom/TriangleSmooth.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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-g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 44%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/ChiralViolationContrib.cpp +[ 44%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-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.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-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.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 44%] Built target rdReducedGraphs -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so +[ 44%] Built target rdCoordGen +[ 44%] Linking CXX executable smaTest1 +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 44%] Built target MolChemicalFeatures -make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake "--color=" +[ 44%] Built target rdMolChemicalFeatures make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 44%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -[ 44%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdMolChemicalFeatures.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp -[ 44%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -[ 44%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp +[ 44%] Built target smaTest1 [ 44%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2023.09.3 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl @@ -4272,167 +4317,158 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 44%] Built target Fingerprints make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" +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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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 -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-202309.3/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu' [ 44%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -[ 44%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp +[ 44%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::UFFConfsHelper(ROMol&, int, int, double, bool)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:49:19: warning: redundant move in return statement [-Wredundant-move] - 49 | return std::move(pyres); - | ~~~~~~~~~^~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:49:19: note: remove 'std::move' call -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::MMFFConfsHelper(ROMol&, int, int, std::string, double, bool)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:66:19: warning: redundant move in return statement [-Wredundant-move] - 66 | return std::move(pyres); - | ~~~~~~~~~^~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:66:19: note: remove 'std::move' call -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::FFConfsHelper(ROMol&, ForceFields::PyForceField&, int, int)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:86:19: warning: redundant move in return statement [-Wredundant-move] - 86 | return std::move(pyres); - | ~~~~~~~~~^~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:86:19: note: remove 'std::move' call +[ 44%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 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.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [ 45%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2023.09.3 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 45%] Linking CXX executable testSLNParse -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 45%] Built target DistGeometry make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake "--color=" +make -f 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/testDistGeom.cpp [ 45%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap/DistGeom.cpp +[ 45%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp +[ 45%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp [ 45%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 45%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/testDistGeom.cpp -[ 45%] Built target testSLNParse -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp: In function 'boost::python::api::object RDKit::GetAtomMatch(boost::python::api::object, int)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:45:19: warning: redundant move in return statement [-Wredundant-move] - 45 | return std::move(res); - | ~~~~~~~~~^~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:45:19: note: remove 'std::move' call -[ 45%] Linking CXX executable smaTest1 -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'boost::python::api::object RDKit::FingerprintWrapper::getBitPathsHelper(const RDKit::AdditionalOutput&)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:452:19: warning: redundant move in return statement [-Wredundant-move] - 452 | return std::move(res); - | ~~~~~~~~~^~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:452:19: note: remove 'std::move' call -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'boost::python::api::object RDKit::FingerprintWrapper::getBitInfoMapHelper(const RDKit::AdditionalOutput&)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:467:19: warning: redundant move in return statement [-Wredundant-move] - 467 | return std::move(res); - | ~~~~~~~~~^~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:467:19: note: remove 'std::move' call -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 45%] Built target smaTest1 -[ 45%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-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.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 45%] Built target rdCoordGen -[ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 45%] Built target rdForceFieldHelpers -[ 45%] Linking CXX executable testDistGeom -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 45%] Built target FilterCatalog +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 45%] Built target testDistGeom -[ 45%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 45%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp +[ 45%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp +[ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::UFFConfsHelper(ROMol&, int, int, double, bool)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:49:19: warning: redundant move in return statement [-Wredundant-move] + 49 | return std::move(pyres); + | ~~~~~~~~~^~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:49:19: note: remove 'std::move' call +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::MMFFConfsHelper(ROMol&, int, int, std::string, double, bool)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:66:19: warning: redundant move in return statement [-Wredundant-move] + 66 | return std::move(pyres); + | ~~~~~~~~~^~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:66:19: note: remove 'std::move' call +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::FFConfsHelper(ROMol&, ForceFields::PyForceField&, int, int)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:86:19: warning: redundant move in return statement [-Wredundant-move] + 86 | return std::move(pyres); + | ~~~~~~~~~^~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:86:19: note: remove 'std::move' call make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 45%] Built target O3AAlign +[ 45%] Built target rdAbbreviations [ 45%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2023.09.3 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.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 45%] 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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/INCHI-API 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/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake "--color=" +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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -MF CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o.d -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDInchiLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDINCHILIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202309.3/External/INCHI-API/inchi.cpp +[ 46%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -MF CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o.d -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp +[ 46%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp +[ 46%] Linking CXX executable testDistGeom +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 46%] Built target testDistGeom +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'boost::python::api::object RDKit::FingerprintWrapper::getBitPathsHelper(const RDKit::AdditionalOutput&)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:452:19: warning: redundant move in return statement [-Wredundant-move] + 452 | return std::move(res); + | ~~~~~~~~~^~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:452:19: note: remove 'std::move' call +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'boost::python::api::object RDKit::FingerprintWrapper::getBitInfoMapHelper(const RDKit::AdditionalOutput&)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:467:19: warning: redundant move in return statement [-Wredundant-move] + 467 | return std::move(res); + | ~~~~~~~~~^~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:467:19: note: remove 'std::move' call +[ 46%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 47%] Built target DistGeom -[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 47%] Built target rdForceFieldHelpers [ 47%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 47%] Built target rdMolChemicalFeatures -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 47%] Built target rdForceField [ 47%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 @@ -4440,11 +4476,6 @@ cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 47%] Built target DistGeomHelpers -[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 47%] Built target rdMHFPFingerprint [ 47%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDInchiLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitRDInchiLib.so.1 -o ../../lib/libRDKitRDInchiLib.so.1.2023.09.3 CMakeFiles/RDInchiLib.dir/inchi.cpp.o /usr/lib/x86_64-linux-gnu/libinchi.so ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl @@ -4464,14 +4495,12 @@ /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 47%] Built target rdDepictor -[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 47%] Built target rdFingerprintGenerator [ 47%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 47%] Built target ChemTransforms @@ -4481,75 +4510,82 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu' +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SDWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDWriter.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/FileParsers/SmilesWriter.cpp +[ 48%] Built target rdMHFPFingerprint +[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_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/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o -MF CMakeFiles/FileParsers.dir/PDBParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PDBParser.cpp +[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/XYZFileParser.cpp -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g 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CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp -[ 50%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdinchi.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdinchi.so CMakeFiles/rdinchi.dir/pyInchi.cpp.o ../../../lib/libRDKitRDInchiLib.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libinchi.so ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 50%] Built target rdinchi [ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl @@ -4563,468 +4599,525 @@ [ 50%] Built target FileParsers make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend -make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend -make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.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-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.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-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/DependInfo.cmake "--color=" -make -f 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build +[ 50%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolDescriptors.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 50%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build +[ 50%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o +[ 50%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_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-202309.3/External/CoordGen/test.cpp +make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Lipinski.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 50%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202309.3/Code/ForceField/UFF/testUFFForceField.cpp +[ 50%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o +make -f 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testChirality.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -MF CMakeFiles/Descriptors.dir/Property.cpp.o.d -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Property.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build +[ 52%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -MF CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o.d -o CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_canon.cpp +make -f Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -MF CMakeFiles/fileParsersTest1.dir/test1.cpp.o.d -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/test1.cpp +[ 55%] Linking CXX executable graphmolSGroupCatch +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 55%] Built target pickleTestsCatch +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-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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+cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testSequence.cpp -[ 55%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/EEM.cpp -[ 55%] Linking CXX executable testMol2ToMol -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -[ 55%] Linking CXX executable testTplParser -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 55%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 55%] Building CXX object 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testSequence.cpp +[ 57%] Linking CXX executable testSGroup +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 55%] Built target testTplParser -[ 55%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/PBF.cpp.o -MF CMakeFiles/Descriptors.dir/PBF.cpp.o.d -o CMakeFiles/Descriptors.dir/PBF.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PBF.cpp +[ 57%] Built target testSGroup make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 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cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -MF CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o.d -o CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 56%] Built target testGeneralFileReader -[ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -MF CMakeFiles/Descriptors.dir/CoulombMat.cpp.o.d -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/CoulombMat.cpp +[ 57%] Built target testExtendedStereoParsing make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers 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CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp +[ 57%] Linking CXX executable testTplParser +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 57%] Built target testTplParser make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp -[ 56%] Linking CXX executable nontetrahedralCatch -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 -[ 56%] Linking CXX executable hanoiTest -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -o nontetrahedralCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -[ 56%] Linking CXX executable pickleTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickleTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -o pickleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -[ 56%] Linking CXX executable graphmoltestPicklerGlobalSetting -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 56%] Built target hanoiTest +[ 57%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 56%] Built target nontetrahedralCatch -[ 57%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o +[ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202309.3/Code/GraphMol/Substruct/test1.cpp +[ 58%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 58%] Built target graphmolSGroupCatch 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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake "--color=" @@ -5033,8 +5126,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -MF CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o.d -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/testChemTransforms.cpp +[ 58%] Linking CXX executable connectTheDotsTest +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 58%] Built target testCoordGen +[ 58%] Built target connectTheDotsTest make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake "--color=" @@ -5043,9 +5139,42 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/catch_tests.cpp -[ 58%] Linking CXX executable canonTestsCatch -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp: In function 'void testMostSubstitutedCoreMatch()': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 1903 | std::make_pair(phenyl.get(), 3u)}) { + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1901:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(orthoMeta.std::unique_ptr::get(), 0)' + 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 1903 | std::make_pair(phenyl.get(), 3u)}) { + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1901:60: note: the temporary was destroyed at the end of the full expression 'std::make_pair(ortho.std::unique_ptr::get(), 1)' + 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 1903 | std::make_pair(phenyl.get(), 3u)}) { + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1902:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(meta.std::unique_ptr::get(), 1)' + 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 1903 | std::make_pair(phenyl.get(), 3u)}) { + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1902:55: note: the temporary was destroyed at the end of the full expression 'std::make_pair(biphenyl.std::unique_ptr::get(), 2)' + 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 1903 | std::make_pair(phenyl.get(), 3u)}) { + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(phenyl.std::unique_ptr::get(), 3)' + 1903 | std::make_pair(phenyl.get(), 3u)}) { + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +[ 58%] Linking CXX executable XYZFileParserCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 58%] Built target XYZFileParserCatchTest 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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake "--color=" @@ -5054,8 +5183,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -MF CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o.d -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp +[ 59%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2023.09.3 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/BCUT.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o CMakeFiles/Descriptors.dir/EEM.cpp.o CMakeFiles/Descriptors.dir/PBF.cpp.o CMakeFiles/Descriptors.dir/PMI.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o CMakeFiles/Descriptors.dir/RDF.cpp.o CMakeFiles/Descriptors.dir/MORSE.cpp.o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o CMakeFiles/Descriptors.dir/WHIM.cpp.o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 59%] Built target canonTestsCatch +[ 59%] Built target Descriptors make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake "--color=" @@ -5064,14 +5197,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o -MF CMakeFiles/testFragCatalog.dir/test1.cpp.o.d -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/test1.cpp -[ 59%] Linking CXX executable testUFFForceField -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -[ 59%] Linking CXX executable testExtendedStereoParsing -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 59%] Linking CXX executable testMolWriter +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 59%] Built target testUFFForceField +[ 59%] Built target testMolWriter make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake "--color=" @@ -5080,403 +5210,581 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp +[ 59%] Linking CXX executable molfileStereoCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -o molfileStereoCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 59%] Built target molfileStereoCatchTest +make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 61%] Linking CXX executable chiralityTestsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 59%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o +[ 61%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp +[ 61%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o -MF CMakeFiles/testMolTransforms.dir/test1.cpp.o.d -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp: In function 'void testMostSubstitutedCoreMatch()': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 1903 | std::make_pair(phenyl.get(), 3u)}) { - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1901:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(orthoMeta.std::unique_ptr::get(), 0)' - 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 1903 | std::make_pair(phenyl.get(), 3u)}) { - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1901:60: note: the temporary was destroyed at the end of the full expression 'std::make_pair(ortho.std::unique_ptr::get(), 1)' - 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 1903 | std::make_pair(phenyl.get(), 3u)}) { - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1902:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(meta.std::unique_ptr::get(), 1)' - 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 1903 | std::make_pair(phenyl.get(), 3u)}) { - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1902:55: note: the temporary was destroyed at the end of the full expression 'std::make_pair(biphenyl.std::unique_ptr::get(), 2)' - 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 1903 | std::make_pair(phenyl.get(), 3u)}) { - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(phenyl.std::unique_ptr::get(), 3)' - 1903 | std::make_pair(phenyl.get(), 3u)}) { - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -[ 60%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp -[ 60%] Linking CXX executable connectTheDotsTest -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 61%] Linking CXX executable testCoulombMat +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 61%] Linking CXX executable testMORSE +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMORSE.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testMORSE.dir/testMORSE.cpp.o -o testMORSE ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 60%] Built target connectTheDotsTest +[ 61%] Built target testCoulombMat make -f 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp +[ 62%] Linking CXX executable testAUTOCORR3D +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 62%] Built target testAUTOCORR3D make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 60%] Linking CXX executable XYZFileParserCatchTest -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 -[ 60%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -[ 60%] Linking CXX executable testMolWriter +[ 62%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 60%] Built target XYZFileParserCatchTest +[ 62%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/catch_tests.cpp +[ 62%] Linking CXX executable test3D +cd /build/reproducible-path/rdkit-202309.3/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 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/testMolAlign.cpp +[ 62%] Linking CXX executable graphmolMolOpsTest +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 62%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/testO3AAlign.cpp +[ 63%] Linking CXX executable testMMFFForceFieldHelpersMultiThread +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 61%] Linking CXX executable filterCatalogTest -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 61%] Built target molfileStereoCatchTest +[ 64%] Built target testDescriptors make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog 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-DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -MF CMakeFiles/FMCS.dir/FMCS.cpp.o.d -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/FMCS.cpp -[ 61%] Linking CXX executable cdxmlParserCatchTest -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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+cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu' +[ 64%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/RascalMCES/RascalMCES.cpp +[ 64%] Linking CXX executable testShapeHelpers +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script 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-DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-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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/build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 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-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-202309.3/Code/GraphMol/FMCS/SubstructMatchCustom.cpp -[ 61%] Linking CXX executable substructTestCatch -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 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executable testMolSupplier -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 63%] Built target rdfragcatalog -[ 63%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 -[ 64%] Linking CXX executable fpGenTestCatch -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -[ 64%] Linking CXX executable graphmoltestChirality -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 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testCrystalForceField -[ 64%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time 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../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 65%] Built target distGeomHelpersCatch make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/DependInfo.cmake "--color=" @@ -5485,11 +5793,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/rapidjson -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -MF CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o.d -o CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/molinterchange_catch.cpp -[ 65%] Linking CXX executable testMolCatalog -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 65%] Linking CXX executable testO3AAlign +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 65%] Built target testMolCatalog +[ 65%] Built target fileParsersCatchTest make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake "--color=" @@ -5498,827 +5806,616 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -MF CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o.d -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/catch_tests.cpp -[ 65%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp -[ 65%] Linking CXX executable testSubstructMatch -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 66%] Built target testSubstructMatch -[ 66%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/Rule1b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp -[ 66%] Linking CXX executable testMMFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -[ 66%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp -[ 66%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/Rule4a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 66%] Linking CXX executable fpTestCatch -cd /build/reproducible-path/rdkit-202309.3/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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+cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-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/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -MF CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/normalize.cpp +[ 68%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /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/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp -[ 67%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 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../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -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-202309.3/obj-x86_64-linux-gnu' -[ 67%] Built target distGeomHelpersCatch -[ 68%] Linking CXX executable trajectoryTest +[ 69%] Linking CXX executable trajectoryTest cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 68%] Linking CXX executable testFingerprintGenerators -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 68%] Built target trajectoryTest -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 68%] Built target testFingerprintGenerators -[ 68%] Linking CXX executable smiTest1 -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -[ 68%] Linking CXX executable testUFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 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/usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 69%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA_UnitTest.cpp +[ 69%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 68%] Built target smiTest1 +[ 69%] Built target trajectoryTest +make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 68%] Built target testUFFForceFieldHelpers -[ 69%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 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/usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 69%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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/usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 69%] Built target rdfragcatalog +[ 69%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 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../../../../rdkit/Chem/rdMolAlign.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 69%] Built target smiTestCatch -[ 69%] Linking CXX executable testCIPLabeler -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 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/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/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 70%] Built target testDistGeomHelpers +[ 70%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/ChemReactions/DaylightParser.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 69%] Built target testCIPLabeler -[ 69%] Linking CXX executable molInterchangeTest1 +[ 70%] Built target rdMolAlign +[ 70%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionPickler.cpp +[ 70%] Linking CXX executable molInterchangeTest1 cd /build/reproducible-path/rdkit-202309.3/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 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../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -[ 69%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2023.09.3 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/BCUT.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o CMakeFiles/Descriptors.dir/EEM.cpp.o CMakeFiles/Descriptors.dir/PBF.cpp.o CMakeFiles/Descriptors.dir/PMI.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o CMakeFiles/Descriptors.dir/RDF.cpp.o CMakeFiles/Descriptors.dir/MORSE.cpp.o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o CMakeFiles/Descriptors.dir/WHIM.cpp.o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 69%] Built target graphmolTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so 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"--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend -make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend -make[4]: 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend -make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/DependInfo.cmake "--color=" -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-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build -make -f External/INCHI-API/CMakeFiles/testInchi.dir/build.make External/INCHI-API/CMakeFiles/testInchi.dir/build -make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build -make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build -make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 70%] Built target molInterchangeTest1 +[ 70%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp +[ 70%] Linking CXX executable testFingerprints +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 70%] Built target testFingerprints +[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp +[ 71%] Linking CXX executable molInterchangeCatchTest +cd /build/reproducible-path/rdkit-202309.3/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -o molInterchangeCatchTest ../../RDGeneral/librdkitCatch.a 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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/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-202309.3/Code/GraphMol/FMCS/SubstructMatchCustom.cpp +[ 71%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' 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CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalCluster.cpp +[ 71%] Linking CXX executable testAbbreviations +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -o testAbbreviations ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitAbbreviations.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp +[ 71%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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/Rule4a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp +[ 71%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/lap_a_la_scipy.cpp.o -MF CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o.d -o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/lap_a_la_scipy.cpp +[ 71%] Linking CXX shared library ../../../lib/libRDKitMolHash.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-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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/usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so 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cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 75%] Built target rdMolHash +[ 75%] Linking CXX executable molHashCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolHash.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 75%] Built target molHashCatchTest +[ 75%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2023.09.3 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -[ 71%] Linking CXX executable molInterchangeCatchTest -cd /build/reproducible-path/rdkit-202309.3/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -o molInterchangeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -[ 72%] Linking CXX executable testDistGeomHelpers -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 72%] Built target FMCS +[ 75%] Built target FMCS make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend -[ 72%] Built target testDistGeomHelpers -make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build +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-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 72%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -MF CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o.d -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/testFMCS_Unit.cpp -[ 72%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 72%] Built target molInterchangeCatchTest -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend +make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build +make[4]: Entering directory 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Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o +[ 75%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 73%] Built target testGETAWAY -[ 74%] Linking CXX executable testAUTOCORR3D -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 74%] Linking CXX executable testAUTOCORR2D -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 74%] Built target testRDF -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 74%] Built target testAUTOCORR3D -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 74%] Built target testAUTOCORR2D -[ 74%] Linking CXX executable fileParsersCatchTest -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so +[ 75%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp: In function 'boost::python::api::object {anonymous}::degenerateSmartsQueryMolDictHelper(const RDKit::MCSResult&)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:646:19: warning: redundant move in return statement [-Wredundant-move] 646 | return std::move(res); | ~~~~~~~~~^~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:646:19: note: remove 'std::move' call -[ 74%] Linking CXX executable testPBF -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPBF.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testPBF.dir/testPBF.cpp.o -o testPBF ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 74%] Built target testPBF -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 74%] Built target fileParsersCatchTest -[ 74%] Linking CXX shared library ../../../lib/libRDKitMolHash.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2023.09.3 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 74%] Linking CXX executable testRDFcustom -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -o testRDFcustom ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2023.09.3 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 74%] Built target MolHash -make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend -make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build -make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 74%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp -[ 74%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202309.3/Code/GraphMol/MolHash/catch_tests.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 74%] Built target testRDFcustom -[ 74%] Linking CXX executable testMolAlign -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 74%] Built target testMolAlign -[ 75%] Linking CXX executable descriptorsTestCatch -cd /build/reproducible-path/rdkit-202309.3/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++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 75%] Built target descriptorsTestCatch -[ 75%] Linking CXX executable test3D -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 75%] Built target test3D -[ 76%] Linking CXX executable FMCStest -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 76%] Built target FMCStest -[ 76%] Linking CXX executable testInchi -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/testInchi.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testInchi.dir/test.cpp.o -o testInchi ../../lib/libRDKitRDInchiLib.so.1.2023.09.3 ../../lib/libRDKitDescriptors.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libinchi.so ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 76%] Linking CXX executable testO3AAlign -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 76%] Built target testInchi -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 76%] Built target testO3AAlign -[ 76%] Linking CXX executable testRascalCluster -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 76%] Built target testRascalCluster -[ 76%] Linking CXX executable fileParsersTest1 -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 76%] Built target fileParsersTest1 -[ 76%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 76%] Built target rdMolHash -[ 76%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 76%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRascalMCES.so CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o ../../../../lib/libRDKitRascalMCES.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 76%] Built target rdMolAlign -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 76%] Built target rdRascalMCES -[ 76%] Linking CXX executable molHashCatchTest -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolHash.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 76%] Built target molHashCatchTest -[ 76%] Linking CXX executable testDescriptors -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 76%] Built target testDescriptors -[ 77%] Linking CXX executable testRascalMCES -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalMCES.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -o testRascalMCES ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so 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-shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so 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CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -c 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-DBOOST_SERIALIZATION_DYN_LINK -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinParser.cpp +[ 75%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinDefs.cpp +[ 75%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o +[ 75%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 77%] Building CXX object 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -MF CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o.d -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -MF CMakeFiles/testReaction.dir/testReaction.cpp.o.d -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testReaction.cpp -[ 79%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -[ 79%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -[ 79%] Building CXX object 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinParser.cpp +make[4]: Entering directory 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/MolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Normalize.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 76%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o +make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build +[ 77%] Building CXX object 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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/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-202309.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 80%] Built target testEnumeration +[ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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-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-202309.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp +[ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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-DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp -[ 82%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp -[ 82%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 82%] Built target MolEnumerator +make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu' +[ 82%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=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-202309.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp [ 82%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp +[ 83%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so +cd /build/reproducible-path/rdkit-202309.3/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++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 82%] Built target graphmolMolOpsTest -[ 82%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 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Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 83%] Building CXX object 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -MF CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o.d -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/deprotectTest.cpp -[ 83%] Linking CXX executable testReactionFingerprints -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 83%] Built target testReactionFingerprints -make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 83%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl In file included from /usr/include/c++/14/algorithm:60, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', @@ -6348,442 +6445,216 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 83%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp -[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 83%] Built target rdMolDescriptors -[ 83%] Linking CXX executable testEnumeration -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 83%] Built target testEnumeration -[ 83%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -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-202309.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp -[ 84%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 84%] Built target MolStandardize +[ 85%] Built target MolStandardize make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend -make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend -make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make 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../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 87%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 87%] Built target molValidateTest -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so +[ 88%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 87%] Built target MarvinParser -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-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.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 -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/DependInfo.cmake "--color=" -[ 87%] Linking CXX executable molFragmentTest -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 +[ 88%] Built target rdmolops +make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build -make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o -MF CMakeFiles/molChargeTest.dir/testCharge.cpp.o.d -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testCharge.cpp +[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -MF CMakeFiles/rdchem.dir/RingInfo.cpp.o.d -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/RingInfo.cpp +[ 88%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -MF CMakeFiles/rdchem.dir/Bond.cpp.o.d -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Bond.cpp -[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -MF CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o.d -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/test2.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 89%] Built target molStandardizeSmallTest -make -f 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Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -MF CMakeFiles/molFragmentTest.dir/testFragment.cpp.o.d -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testFragment.cpp +[ 88%] Linking CXX executable molStandardizeTest +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 90%] Built target molNormalizeTest -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend +[ 88%] Built target molStandardizeTest +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp -[ 90%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202309.3/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++ 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/usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c 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'/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 94%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -MF CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o.d -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp -[ 94%] Linking CXX executable rxnTestCatch -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection 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../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 94%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake 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../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp +[ 88%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -MF CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o.d -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp +[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/EditableMol.cpp.o -MF CMakeFiles/rdchem.dir/EditableMol.cpp.o.d -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/EditableMol.cpp +[ 89%] Linking CXX executable molChargeTest +cd 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../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 94%] Built target TautomerQuery +[ 89%] Built target molChargeTest make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 94%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o +[ 89%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 98%] Linking CXX executable testMrvToMol -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMrvToMol.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -o testMrvToMol ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 98%] Built target molTautomerTest -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 98%] Built target testMrvToMol -[ 98%] Linking CXX executable molStandardizeCatchTest -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 98%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 98%] Linking CXX executable testMolEnumerator -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 -[ 98%] Built target molStandardizeCatchTest -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 98%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 98%] Built target testMolEnumerator -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 98%] Built target rdMolStandardize -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 98%] Built target rdmolops -[ 98%] Linking CXX executable tautomerQueryTestCatch -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 98%] Built target tautomerQueryTestCatch +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/Wrap/MonomerInfo.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, @@ -6831,21 +6702,191 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable testScaffoldNetwork -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include 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CMakeFiles/rdchem.dir/MolBundle.cpp.o.d -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolBundle.cpp +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 89%] Built target molStandardizeSmallTest +make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 89%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o +cd 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/StereoGroup.cpp.o -MF CMakeFiles/rdchem.dir/StereoGroup.cpp.o.d -o CMakeFiles/rdchem.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/StereoGroup.cpp +[ 89%] Linking CXX executable molFragmentTest +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -MF CMakeFiles/moldraw2DTest1.dir/test1.cpp.o.d -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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&& /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 89%] Built target ScaffoldNetwork +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 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Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection 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../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so /usr/lib/x86_64-linux-gnu/libboost_system.so 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../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl @@ -6853,31 +6894,46 @@ make[4]: Leaving directory 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -MF CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/catch_tests.cpp +[ 99%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so +cd 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/usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl @@ -6885,92 +6941,67 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Built target RGroupDecomposition make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp [ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 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/usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -[ 99%] Linking CXX executable testRGroupDecompInternals -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 99%] Built target rdMolDraw2D +[ 99%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 99%] Built target testRGroupDecompInternals +[ 99%] Built target rdGeneralizedSubstruct make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 99%] Built target rdchem +[ 99%] Built target rdMolStandardize [ 99%] Linking CXX executable generalizedSubstructCatch cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -o generalizedSubstructCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Built target generalizedSubstructCatch -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeneralizedSubstruct.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdGeneralizedSubstruct.so CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 99%] Built target rdGeneralizedSubstruct -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-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.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 99%] Built target rdChemReactions -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[ 99%] Linking CXX executable testRGroupDecompInternals +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 99%] Built target rdMolDraw2D +[ 99%] Built target testRGroupDecompInternals [ 99%] Linking CXX executable rgroupCatchTests cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Built target rgroupCatchTests -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../../lib/libRDKitga.so.1.2023.09.3 ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 99%] Built target rdRGroupDecomposition -[ 99%] Linking CXX executable testReaction -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[ 99%] Built target testReaction [ 99%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so @@ -6978,51 +7009,56 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] 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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/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-202309.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o [100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -[100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/catch_tests.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp [100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202309.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp +[100%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../../lib/libRDKitga.so.1.2023.09.3 ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[100%] Built target rdRGroupDecomposition [100%] Linking CXX executable moldraw2DTestCatch cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [100%] Built target moldraw2DTestCatch -[100%] Linking CXX executable testRGroupDecomp -cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[100%] Built target testRGroupDecomp -[100%] Linking CXX executable substructLibraryCatchTest -cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl [100%] Linking CXX executable substructLibraryTest cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[100%] Linking CXX executable substructLibraryCatchTest +cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' +[100%] Linking CXX executable testRGroupDecomp +cd /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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 CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl +[100%] Built target substructLibraryTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' [100%] Built target substructLibraryCatchTest make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -[100%] Built target substructLibraryTest +[100%] Built target testRGroupDecomp [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202309.3/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-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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,-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.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libpython3.12.so /usr/lib/x86_64-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so -ldl @@ -7329,73 +7365,73 @@ Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/libs Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/data +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/tutorial +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/data +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DetermineBonds Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Fonts Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt/Demo -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Fonts +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/tutorial -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DetermineBonds -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/libs Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Catalogs Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/DataStructs Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Query Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML/Cluster Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML/Cluster/Murtagh -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/DataManip Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers @@ -7408,8 +7444,8 @@ Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics/EigenSolvers +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Geometry Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Features @@ -8470,8 +8506,6 @@ Generating code for file RegisterDescriptor.h... Generating code for file USRDescriptor.h... Generating code for file WHIM.h... -Generating code for file details.h... -Generating code for file details.h... Generating code for file DetermineBonds.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Embedder.h... @@ -8586,6 +8620,8 @@ Generating code for file mf.h... Generating code for file MolHash.h... Generating code for file nmmolhash.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... @@ -8600,6 +8636,8 @@ Generating code for file Metal.h... Generating code for file MolStandardize.h... Generating code for file Normalize.h... +Generating code for file Tautomer.h... +Generating code for file Tautomer.h... Generating code for file TautomerCatalogEntry.h... Generating code for file TautomerCatalogParams.h... Generating code for file TautomerCatalogUtils.h... @@ -8660,8 +8698,6 @@ Generating code for file StripSmallFragments.h... Generating code for file StructChecker.h... Generating code for file StructCheckerOptions.h... -Generating code for file Tautomer.h... -Generating code for file Tautomer.h... Generating code for file Utilites.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... @@ -8883,8 +8919,6 @@ Generating docs for file RegisterDescriptor.h... Generating docs for file USRDescriptor.h... Generating docs for file WHIM.h... -Generating docs for file details.h... -Generating docs for file details.h... Generating docs for file DetermineBonds.h... Generating docs for file BoundsMatrixBuilder.h... Generating docs for file Embedder.h... @@ -8999,6 +9033,8 @@ Generating docs for file mf.h... Generating docs for file MolHash.h... Generating docs for file nmmolhash.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... @@ -9013,6 +9049,8 @@ Generating docs for file Metal.h... Generating docs for file MolStandardize.h... Generating docs for file Normalize.h... +Generating docs for file Tautomer.h... +Generating docs for file Tautomer.h... Generating docs for file TautomerCatalogEntry.h... Generating docs for file TautomerCatalogParams.h... Generating docs for file TautomerCatalogUtils.h... @@ -9025,11 +9063,11 @@ Generating docs for file new_canon.h... Generating docs for file GasteigerCharges.h... Generating docs for file GasteigerParams.h... -Generating docs for file PeriodicTable.h... -Generating docs for file QueryAtom.h... -Generating do/build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' +Generating docs for/build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:534: warning: Found unknown command '\overloadquery' -cs for file QueryBond.h... + file PeriodicTable.h... +Generating docs for file QueryAtom.h... +Generating docs for file QueryBond.h... Generating docs for file QueryOps.h... Generating docs for file PartitionSet.h... Generating docs for file RascalClusterOptions.h... @@ -9075,8 +9113,6 @@ Generating docs for file StripSmallFragments.h... Generating docs for file StructChecker.h... Generating docs for file StructCheckerOptions.h... -Generating docs for file Tautomer.h... -Generating docs for file Tautomer.h... Generating docs for file Utilites.h... Generating docs for file Subgraphs.h... Generating docs for file SubgraphUtils.h... @@ -11707,10 +11743,10 @@ /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so #export RDBASE=/build/reproducible-path/rdkit-202309.3 PYTHONPATH=/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu//lib:" PYTHONPATH=/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/:/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu//lib:" dh_auto_test - cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 + cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j42 +/usr/bin/ctest --force-new-ctest-process --verbose -j20 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. @@ -11843,147 +11879,15 @@ 20: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/testMatrices 20: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics 20: Test timeout computed to be: 1500 -test 21 - Start 21: testConrec - -21: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/testConrec -21: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics -21: Test timeout computed to be: 1500 -test 22 - Start 22: testAlignment - -22: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/testAlignment -22: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment -22: Test timeout computed to be: 1500 -test 23 - Start 23: pyAlignment - -23: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/Wrap/testAlignment.py" -23: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap -23: Test timeout computed to be: 1500 -test 24 - Start 24: testOptimizer - -24: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/testOptimizer -24: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer -24: Test timeout computed to be: 1500 -test 25 - Start 25: testUFFForceField - -25: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/UFF/testUFFForceField -25: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/UFF -25: Test timeout computed to be: 1500 -test 26 - Start 26: testMMFFForceField - -26: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField -26: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF -26: Test timeout computed to be: 1500 -test 27 - Start 27: pyForceFieldConstraints - -27: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/ForceField/Wrap/testConstraints.py" -27: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/Wrap -27: Test timeout computed to be: 1500 -test 28 - Start 28: testDistGeom - -28: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom/testDistGeom -28: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom -28: Test timeout computed to be: 1500 -test 29 - Start 29: pyDistGeom - -29: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap/rough_test.py" -29: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom/Wrap -29: Test timeout computed to be: 1500 -test 30 - Start 30: graphmolTest1 - -30: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -30: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -30: Test timeout computed to be: 1500 -test 31 - Start 31: graphmolcpTest - -31: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolcpTest -31: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -31: Test timeout computed to be: 1500 -test 32 - Start 32: graphmolqueryTest - -32: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest -32: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -32: Test timeout computed to be: 1500 -test 33 - Start 33: graphmolMolOpsTest - -33: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMolOpsTest -33: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -33: Test timeout computed to be: 1500 -test 34 - Start 34: graphmoltestChirality - -34: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestChirality -34: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -34: Test timeout computed to be: 1500 -test 35 - Start 35: graphmoltestPickler - -35: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPickler -35: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -35: Test timeout computed to be: 1500 -test 36 - Start 36: graphmoltestPicklerGlobalSetting - -36: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting -36: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -36: Test timeout computed to be: 1500 -test 37 - Start 37: graphmolIterTest - -37: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolIterTest -37: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -37: Test timeout computed to be: 1500 -test 38 - Start 38: hanoiTest - -38: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest -38: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -38: Test timeout computed to be: 1500 -test 39 - Start 39: graphmolMemTest1 - -39: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 -39: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -39: Test timeout computed to be: 1500 -test 40 - Start 40: resMolSupplierTest - -40: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest -40: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -40: Test timeout computed to be: 1500 -test 41 - Start 41: molBundleTest - -41: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/molBundleTest -41: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -41: Test timeout computed to be: 1500 -test 42 - Start 42: testSGroup - -42: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/testSGroup -42: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -42: Test timeout computed to be: 1500 -1: [07:34:57] ------------------------------------- -1: [07:34:57] ------------------------------------- -1: [07:34:57] ------------------------------------- -1: [07:34:57] ------------------------------------- -1: [07:34:57] Extended double-bond stereochemistry (e.g. C=C=C=C) ignored -1: [07:34:57] ------------------------------------- -1: [07:34:57] ------------------------------------- -1: [07:34:57] ------------------------------------- -1: [07:34:57] Test multithreading +1: [04:03:45] ------------------------------------- +1: [04:03:45] ------------------------------------- +1: [04:03:45] ------------------------------------- +1: [04:03:45] ------------------------------------- +1: [04:03:45] Extended double-bond stereochemistry (e.g. C=C=C=C) ignored +1: [04:03:45] ------------------------------------- +1: [04:03:45] ------------------------------------- +1: [04:03:45] ------------------------------------- +1: [04:03:45] Test multithreading 1: reading molecules 1: generating reference data 1: processing @@ -11991,6 +11895,35 @@ 1: launch :1 1: launch :2 1: launch :3 +1: [04:03:45] +1: +1: **** +1: Test Assert +1: Expression Failed: +1: Violation occurred on line 41 in file ./External/INCHI-API/test.cpp +1: Failed Expression: inchi == inchis[i] +1: **** +1: +1: [04:03:45] +1: +1: **** +1: Test Assert +1: Expression Failed: +1: Violation occurred on line 41 in file ./External/INCHI-API/test.cpp +1: Failed Expression: inchi == inchis[i] +1: **** +1: +1: [04:03:45] +1: +1: **** +1: Test Assert +1: Expression Failed: +1: Violation occurred on line 41 in file ./External/INCHI-API/test.cpp +1: Failed Expression: inchi == inchis[i] +1: **** +1: +1: terminate called after throwing an instance of 'Invar::Invariant' +1: what(): Expression Failed: 2: core 2: RDKit 2D 2: @@ -12448,13 +12381,13 @@ 2: 2 5 1 0 2: M END 2: -4: [07:34:57] Testing Github940: property dictionaries leaking memory -4: [07:34:57] done +4: [04:03:45] Testing Github940: property dictionaries leaking memory +4: [04:03:45] done 4: Testing RDValue 4: Testing RDAny 4: dict set int vect 4: dict get int vect -4: static boost any:0.073907 s +4: static boost any:0.138116 s 5: -- running tests -- 5: min: -2147483648 -2147483648 5: min: 0 0 @@ -12467,28 +12400,28 @@ 5: == unsigned int 5: == bool 5: == std::string -6: [07:34:57] +6: [04:03:45] 6: ----------------------------------------- -6: [07:34:57] Finished: testPushAndPop() -6: [07:34:57] +6: [04:03:45] Finished: testPushAndPop() +6: [04:03:45] 6: ----------------------------------------- -6: [07:34:57] +6: [04:03:45] 6: ----------------------------------------- -7: Randomness seeded to: 2700800175 +7: Randomness seeded to: 3471192681 7: =============================================================================== 7: All tests passed (32 assertions in 2 test cases) 7: -8: [07:34:57] should not be silent -8: [07:34:57] should not be silent -8: Randomness seeded to: 1090587886 -8: [07:34:57] should not be silent -8: [07:34:57] should not be silent -8: [07:34:57] should not be silent -8: [07:34:57] should not be silent -8: [07:34:57] should not be silent -8: [07:34:57] should not be silent -8: [07:34:57] should not be silent -8: [07:34:57] should not be silent +8: [04:03:45] should not be silent +8: [04:03:45] should not be silent +8: Randomness seeded to: 2710372409 +8: [04:03:45] should not be silent +8: [04:03:45] should not be silent +8: [04:03:45] should not be silent +8: [04:03:45] should not be silent +8: [04:03:45] should not be silent +8: [04:03:45] should not be silent +8: [04:03:45] should not be silent +8: [04:03:45] should not be silent 8: =============================================================================== 8: All tests passed (26 assertions in 3 test cases) 8: @@ -12516,8 +12449,8 @@ 16: testPointOps2D 16: **************************************** 16: test12D -16: ref1: 1.76094 3.98375 ref2: 3.78665 2.95704 -16: pt1: 3.34199 3.4142 pt2: 4.33581 1.08962 +16: ref1: 1.19792 1.30668 ref2: 1.75787 2.78519 +16: pt1: 3.34284 2.60034 pt2: 1.79866 2.51379 16: **************************************** 16: test23D 16: **************************************** @@ -12532,6 +12465,123 @@ 16: **************************************** 16: testFromQuaternion 16: **************************************** +18: Randomness seeded to: 1920773492 +18: =============================================================================== +18: All tests passed (50 assertions in 5 test cases) +18: + 1/223 Test #5: testRDValue ............................ Passed 0.15 sec + 2/223 Test #7: dictTestsCatch ......................... Passed 0.14 sec + 3/223 Test #8: logTestsCatch .......................... Passed 0.14 sec + 4/223 Test #9: testDataStructs ........................ Passed 0.13 sec + 5/223 Test #10: testFPB ................................ Passed 0.13 sec + 6/223 Test #11: testMultiFPB ........................... Passed 0.12 sec + 7/223 Test #16: testTransforms ......................... Passed 0.08 sec + 8/223 Test #18: geometryTestsCatch ..................... Passed 0.05 sec +test 21 + Start 21: testConrec + +21: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/testConrec +21: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics +21: Test timeout computed to be: 1500 +test 22 + Start 22: testAlignment + +22: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/testAlignment +22: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment +22: Test timeout computed to be: 1500 +test 23 + Start 23: pyAlignment + +23: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/Wrap/testAlignment.py" +23: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap +23: Test timeout computed to be: 1500 +test 24 + Start 24: testOptimizer + +24: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/testOptimizer +24: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer +24: Test timeout computed to be: 1500 +test 25 + Start 25: testUFFForceField + +25: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/UFF/testUFFForceField +25: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/UFF +25: Test timeout computed to be: 1500 +test 26 + Start 26: testMMFFForceField + +26: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField +26: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF +26: Test timeout computed to be: 1500 +test 27 + Start 27: pyForceFieldConstraints + +27: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/ForceField/Wrap/testConstraints.py" +27: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ForceField/Wrap +27: Test timeout computed to be: 1500 +test 28 + Start 28: testDistGeom + +28: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom/testDistGeom +28: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom +28: Test timeout computed to be: 1500 + 9/223 Test #1: testInchi ..............................Subprocess aborted***Exception: 0.28 sec +[04:03:45] ------------------------------------- +[04:03:45] ------------------------------------- +[04:03:45] ------------------------------------- +[04:03:45] ------------------------------------- +[04:03:45] Extended double-bond stereochemistry (e.g. C=C=C=C) ignored +[04:03:45] ------------------------------------- +[04:03:45] ------------------------------------- +[04:03:45] ------------------------------------- +[04:03:45] Test multithreading +reading molecules +generating reference data +processing + launch :0 + launch :1 + launch :2 + launch :3 +[04:03:45] + +**** +Test Assert +Expression Failed: +Violation occurred on line 41 in file ./External/INCHI-API/test.cpp +Failed Expression: inchi == inchis[i] +**** + +[04:03:45] + +**** +Test Assert +Expression Failed: +Violation occurred on line 41 in file ./External/INCHI-API/test.cpp +Failed Expression: inchi == inchis[i] +**** + +[04:03:45] + +**** +Test Assert +Expression Failed: +Violation occurred on line 41 in file ./External/INCHI-API/test.cpp +Failed Expression: inchi == inchis[i] +**** + +terminate called after throwing an instance of 'Invar::Invariant' + what(): Expression Failed: + +20: [04:03:45] ----------------------------------------- +20: [04:03:45] Testing RDNumerics: vectors and matrices Code +20: [04:03:45] --------------------------------------- +20: [04:03:45] test1Vector +20: [04:03:45] --------------------------------------- +20: [04:03:45] test2Matrix +20: [04:03:45] --------------------------------------- +20: [04:03:45] test3SquareMatrix +20: [04:03:45] --------------------------------------- +20: [04:03:45] test4SymmMatrix 17: *********************************************************** 17: Testing Grid 17: --------------------------------- @@ -12549,21 +12599,7 @@ 17: --------------------------------- 17: testUniformGridIndexing 17: -18: Randomness seeded to: 1804681434 -18: =============================================================================== -18: All tests passed (50 assertions in 5 test cases) -18: -20: [07:34:57] ----------------------------------------- -20: [07:34:57] Testing RDNumerics: vectors and matrices Code -20: [07:34:57] --------------------------------------- -20: [07:34:57] test1Vector -20: [07:34:57] --------------------------------------- -20: [07:34:57] test2Matrix -20: [07:34:57] --------------------------------------- -20: [07:34:57] test3SquareMatrix -20: [07:34:57] --------------------------------------- -20: [07:34:57] test4SymmMatrix -21: Randomness seeded to: 1503316689 +21: Randomness seeded to: 2051745085 21: =============================================================================== 21: All tests passed (76 assertions in 3 test cases) 21: @@ -12630,9 +12666,47 @@ 25: done 25: ------------------------------------- 25: Unit tests for all UFF constraint terms. -25: done -25: ------------------------------------- -25: Unit tests for copying UFF ForceFields. + 10/223 Test #17: testGrid ............................... Passed 0.19 sec + 11/223 Test #20: testMatrices ........................... Passed 0.13 sec + 12/223 Test #21: testConrec ............................. Passed 0.11 sec + 13/223 Test #22: testAlignment .......................... Passed 0.10 sec + 14/223 Test #24: testOptimizer .......................... Passed 0.08 sec +test 29 + Start 29: pyDistGeom + +29: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap/rough_test.py" +29: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DistGeom/Wrap +29: Test timeout computed to be: 1500 +test 30 + Start 30: graphmolTest1 + +30: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +30: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +30: Test timeout computed to be: 1500 +test 31 + Start 31: graphmolcpTest + +31: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolcpTest +31: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +31: Test timeout computed to be: 1500 +test 32 + Start 32: graphmolqueryTest + +32: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +32: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +32: Test timeout computed to be: 1500 +test 33 + Start 33: graphmolMolOpsTest + +33: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMolOpsTest +33: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +33: Test timeout computed to be: 1500 +test 34 + Start 34: graphmoltestChirality + +34: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestChirality +34: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +34: Test timeout computed to be: 1500 26: ------------------------------------- 26: Official MMFF validation suite. 28: *********************************************************** @@ -12646,713 +12720,6 @@ 28: 1 1 1 0 28: *********************************************************** 28: -30: Atoms: -30: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 0 arom?: 0 chi: 0 -30: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 -30: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 0 arom?: 0 chi: 0 -30: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 -30: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 -30: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 -30: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: 0 arom?: 0 chi: 0 -30: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: 0 arom?: 1 chi: 0 -30: 8 22 Ti chg: 0 deg: 1 exp: [07:34:57] -30: -30: **** -30: Pre-condition Violation -30: getExplicitValence() called without call to calcExplicitValence() -30: Violation occurred on line 298 in file ./Code/GraphMol/Atom.cpp -30: Failed Expression: d_explicitValence > -1 -30: **** -30: -30: N/A imp: -1 hyb: 0 arom?: 0 chi: 0 -30: Bonds: -30: 0 0->1 order: 1 conj?: 0 aromatic?: 0 -30: 1 1->2 order: 2 conj?: 0 aromatic?: 0 -30: 2 2->3 order: 1 conj?: 0 aromatic?: 0 -30: 3 0->4 order: 1 conj?: 0 aromatic?: 0 -30: 4 5->6 order: 3 conj?: 0 aromatic?: 0 -30: 5 6->7 order: 1 conj?: 0 aromatic?: 0 -30: 6 7->8 order: 2 conj?: 0 aromatic?: 0 -30: [07:34:57] -30: -30: **** -30: Pre-condition Violation -30: bond already exists -30: Violation occurred on line 380 in file ./Code/GraphMol/RWMol.cpp -30: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) -30: **** -30: -30: [07:34:57] -30: -30: **** -30: Pre-condition Violation -30: bond already exists -30: Violation occurred on line 380 in file ./Code/GraphMol/RWMol.cpp -30: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) -30: **** -30: -30: [07:34:57] -30: -30: **** -30: Pre-condition Violation -30: attempt to add self-bond -30: Violation occurred on line 379 in file ./Code/GraphMol/RWMol.cpp -30: Failed Expression: atomIdx1 != atomIdx2 -30: **** -30: -30: [07:34:57] -30: -30: **** -30: Pre-condition Violation -30: bond already exists -30: Violation occurred on line 441 in file ./Code/GraphMol/ROMol.cpp -30: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) -30: **** -30: -30: [07:34:57] -30: -30: **** -30: Pre-condition Violation -30: attempt to add self-bond -30: Violation occurred on line 439 in file ./Code/GraphMol/ROMol.cpp -30: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() -30: **** -30: -30: [07:34:57] Explicit valence for atom # 0 B, 4, is greater than permitted -30: [07:34:57] Explicit valence for atom # 0 B, 5, is greater than permitted -30: [07:34:57] -30: -30: **** -30: Post-condition Violation -30: Element 'Xx' not found -30: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -30: Failed Expression: anum > -1 -30: **** -30: -30: [07:34:57] ------------------------------------- -30: [07:34:57] Test github381: thread-safe initialization of the periodic table -30: [07:34:57] done -30: [07:34:57] ------------------------------------- -30: [07:34:57] Test github1041: Segfault for atom with no owner (expect some warnings) -30: [07:34:57] -30: -30: **** -30: Pre-condition Violation -30: no owner -30: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -30: Failed Expression: dp_mol -30: **** -30: -30: [07:34:57] -30: -30: **** -30: Pre-condition Violation -30: no owner -30: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h -30: Failed Expression: dp_mol -30: **** -30: -30: [07:34:57] done -30: [07:34:57] ------------------------------------- -30: [07:34:57] Test github1041: Segfault for atom with no owner (expect some warnings) -30: [07:34:57] -30: -30: **** -30: Pre-condition Violation -30: no owner -30: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -30: Failed Expression: dp_mol -30: **** -30: -30: [07:34:57] -30: -30: **** -30: Pre-condition Violation -30: no owner -30: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h -30: Failed Expression: dp_mol -30: **** -30: -30: [07:34:57] done -30: [07:34:57] ------------------------------------- -30: [07:34:57] Test github1453: RWMol.clear() should reset the numBonds count. -30: [07:34:57] done -30: [07:34:57] ------------------------------------- -30: [07:34:57] Test range-based for loops. -30: [07:34:57] done -30: [07:34:57] ------------------------------------- -30: [07:34:57] Test github1642: Atom index type is too low for big molecules. -31: -31: -31: -31: COPY -32: [07:34:57] ---------------------- Test1 -32: [07:34:57] Done! -32: [07:34:57] ---------------------- Test2 -32: [07:34:57] Done! -32: [07:34:57] ---------------------- Test3 -32: [07:34:57] Done! -32: [07:34:57] ---------------------- Test4 -32: [07:34:57] Done! -32: [07:34:57] ---------------------- Test5 -32: [07:34:57] Done! -32: [07:34:57] Done! -32: [07:34:57] ---------------------- Test issue 2892580 -32: [07:34:57] Done! -32: [07:34:57] ---------------------- Test github issue 53: query molecules not matching [R] -32: [07:34:57] Done! -32: [07:34:57] ---------------------- Test queries using qualifiers instead of == -32: [07:34:57] Done! -32: [07:34:57] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -32: [07:34:57] Done! -32: [07:34:57] ---------------------- Test extra atom queries -32: [07:34:57] Done! -32: [07:34:57] ---------------------- Test extra bond queries -32: [07:34:57] Done! -32: [07:34:57] ---------------------- Test num heteroatom neighbor queries -32: [07:34:57] Done! -32: [07:34:57] ---------------------- Test atom type queries -32: [07:34:57] Done! -32: [07:34:57] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -32: [07:34:57] Done! -32: [07:34:57] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -32: [07:34:57] Done! -33: 1 1 2 -33: 1 1 1 -33: 2 1 0.75 -33: path: 2 -33: [07:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -33: [07:34:57] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 13 ignored -33: [07:34:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -33: [07:34:57] Explicit valence for atom # 0 B, 5, is greater than permitted -33: [07:34:57] Explicit valence for atom # 1 C, 5, is greater than permitted -33: [07:34:57] Explicit valence for atom # 1 C, 5, is greater than permitted -33: [07:34:57] Explicit valence for atom # 1 C, 5, is greater than permitted -33: [07:34:57] Explicit valence for atom # 1 Si, 7, is greater than permitted -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing String Pickle Roundtrips. - 1/223 Test #5: testRDValue ............................ Passed 0.09 sec - 2/223 Test #7: dictTestsCatch ......................... Passed 0.08 sec - 3/223 Test #8: logTestsCatch .......................... Passed 0.08 sec - 4/223 Test #9: testDataStructs ........................ Passed 0.08 sec - 5/223 Test #10: testFPB ................................ Passed 0.08 sec - 6/223 Test #11: testMultiFPB ........................... Passed 0.08 sec - 7/223 Test #16: testTransforms ......................... Passed 0.07 sec - 8/223 Test #17: testGrid ............................... Passed 0.07 sec - 9/223 Test #18: geometryTestsCatch ..................... Passed 0.07 sec - 10/223 Test #20: testMatrices ........................... Passed 0.07 sec - 11/223 Test #21: testConrec ............................. Passed 0.07 sec - 12/223 Test #22: testAlignment .......................... Passed 0.06 sec - 13/223 Test #24: testOptimizer .......................... Passed 0.06 sec - 14/223 Test #28: testDistGeom ........................... Passed 0.05 sec - 15/223 Test #31: graphmolcpTest ......................... Passed 0.05 sec - 16/223 Test #32: graphmolqueryTest ...................... Passed 0.05 sec -test 43 - Start 43: test-valgrind - -43: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/test-valgrind -43: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -43: Test timeout computed to be: 1500 -test 44 - Start 44: graphmolTestsCatch - -44: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -44: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -44: Test timeout computed to be: 1500 -test 45 - Start 45: graphmolOrganometallicsCatch - -45: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch -45: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -45: Test timeout computed to be: 1500 -test 46 - Start 46: graphmolSGroupCatch - -46: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolSGroupCatch -46: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -46: Test timeout computed to be: 1500 -test 47 - Start 47: graphmolAdjustQueryCatch - -47: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch -47: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -47: Test timeout computed to be: 1500 -test 48 - Start 48: chiralityTestsCatch - -48: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/chiralityTestsCatch -48: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -48: Test timeout computed to be: 1500 -test 49 - Start 49: canonTestsCatch - -49: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/canonTestsCatch -49: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -49: Test timeout computed to be: 1500 -test 50 - Start 50: moliteratorTestsCatch - -50: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/moliteratorTestsCatch -50: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -50: Test timeout computed to be: 1500 -test 51 - Start 51: queryTestsCatch - -51: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/queryTestsCatch -51: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -51: Test timeout computed to be: 1500 -test 52 - Start 52: molbundleTestsCatch - -52: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/molbundleTestsCatch -52: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -52: Test timeout computed to be: 1500 -test 53 - Start 53: pickleTestsCatch - -53: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/pickleTestsCatch -53: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol -53: Test timeout computed to be: 1500 -test 54 - Start 54: smiTest1 - -54: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 -54: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -54: Test timeout computed to be: 1500 -test 55 - Start 55: smiTest2 - -55: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 -55: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -55: Test timeout computed to be: 1500 -test 56 - Start 56: cxsmilesTest - -56: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest -56: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -56: Test timeout computed to be: 1500 -test 57 - Start 57: smaTest1 - -57: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 -57: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -57: Test timeout computed to be: 1500 -test 58 - Start 58: smiTestCatch - -58: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -58: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -58: Test timeout computed to be: 1500 -1: [07:34:57] -1: -1: **** -1: Test Assert -1: Expression Failed: -1: Violation occurred on line 41 in file ./External/INCHI-API/test.cpp -1: Failed Expression: inchi == inchis[i] -1: **** -1: -1: [07:34:57] Invalid InChI prefix in generating InChI Key -1: [07:34:57] -1: -1: **** -1: Test Assert -1: Expression Failed: -1: Violation occurred on line 45 in file ./External/INCHI-API/test.cpp -1: Failed Expression: key2 == keys[i] -1: **** -1: -1: [07:34:57] -1: -1: **** -1: Test Assert -1: Expression Failed: -1: Violation occurred on line 41 in file ./External/INCHI-API/test.cpp -1: Failed Expression: inchi == inchis[i] -1: **** -1: -25: done -25: ------------------------------------- -25: Unit test for UFF butane scan. -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing reading existing pickle file (v2). -34: -------------------------- -34: -------------------------- -34: C/C=C/C(C)Cl -34: [07:34:57] Conflicting single bond directions around double bond at index 2. -34: [07:34:57] BondStereo set to STEREONONE and single bond directions set to NONE. -34: [07:34:57] Conflicting single bond directions around double bond at index 4. -34: [07:34:57] BondStereo set to STEREONONE and single bond directions set to NONE. -34: [07:34:57] Conflicting single bond directions around double bond at index 15. -34: [07:34:57] BondStereo set to STEREONONE and single bond directions set to NONE. -34: [07:34:57] Conflicting single bond directions around double bond at index 2. -34: [07:34:57] BondStereo set to STEREONONE and single bond directions set to NONE. -34: [07:34:57] Conflicting single bond directions around double bond at index 1. -34: [07:34:57] BondStereo set to STEREONONE and single bond directions set to NONE. -34: -------------------------------------------------- - 17/223 Test #39: graphmolMemTest1 ....................... Passed 0.07 sec - 18/223 Test #37: graphmolIterTest ....................... Passed 0.07 sec -36: [07:34:57] done - 19/223 Test #36: graphmoltestPicklerGlobalSetting ....... Passed 0.08 sec - 20/223 Test #41: molBundleTest .......................... Passed 0.07 sec -44: Randomness seeded to: 2401343911 -44: [07:34:57] WARNING: not removing hydrogen atom without neighbors -44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -44: [07:34:57] Explicit valence for atom # 1 N, 5, is greater than permitted -44: [07:34:57] Explicit valence for atom # 1 N, 6, is greater than permitted -44: [07:34:57] Explicit valence for atom # 1 N, 5, is greater than permitted -44: [07:34:57] Explicit valence for atom # 1 N, 5, is greater than permitted -44: [07:34:57] Explicit valence for atom # 2 O, 3, is greater than permitted -44: [07:34:57] Explicit valence for atom # 2 O, 3, is greater than permitted -44: [07:34:57] non-ring atom 2 marked aromatic -44: [07:34:57] non-ring atom 2 marked aromatic -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 1 2 3 -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 1 2 3 -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 -44: [07:34:57] Explicit valence for atom # 1 O, 3, is greater than permitted -44: [07:34:57] Explicit valence for atom # 4 F, 2, is greater than permitted -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 -44: [07:34:57] Explicit valence for atom # 1 C, 5, is greater than permitted -44: [07:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors -44: [07:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors -44: [07:34:57] WARNING: not removing hydrogen atom with wedged bond -44: [07:34:57] WARNING: not removing hydrogen atom without neighbors -44: [07:34:57] WARNING: not removing hydrogen atom without neighbors -46: Randomness seeded to: 2001951807 -46: =============================================================================== -46: All tests passed (120 assertions in 6 test cases) -46: -50: Randomness seeded to: 3120086680 -50: =============================================================================== -50: All tests passed (14 assertions in 4 test cases) -50: - 21/223 Test #34: graphmoltestChirality .................. Passed 0.09 sec - 22/223 Test #42: testSGroup ............................. Passed 0.07 sec - 23/223 Test #43: test-valgrind .......................... Passed 0.05 sec - 24/223 Test #46: graphmolSGroupCatch .................... Passed 0.04 sec -test 59 - Start 59: nontetrahedralCatch - -59: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch -59: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -59: Test timeout computed to be: 1500 -test 60 - Start 60: testDepictor - -60: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor -60: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor -60: Test timeout computed to be: 1500 -test 61 - Start 61: depictorCatch - -61: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch -61: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor -61: Test timeout computed to be: 1500 -test 62 - Start 62: pyDepictor - -62: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap/testDepictor.py" -62: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap -62: Test timeout computed to be: 1500 -test 63 - Start 63: testMrvToMol - -63: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -63: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse -63: Test timeout computed to be: 1500 -test 64 - Start 64: fileParsersTest1 - -64: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -64: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -64: Test timeout computed to be: 1500 -test 65 - Start 65: testMolSupplier - -65: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -65: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -65: Test timeout computed to be: 1500 -test 66 - Start 66: testGeneralFileReader - -66: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -66: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -66: Test timeout computed to be: 1500 -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing combining molecules using pickles. -35: Atoms: -35: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 -35: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 -35: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 -35: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 -35: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 -35: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 4 arom?: 0 chi: 0 -35: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 -35: Bonds: -35: 0 0->1 order: 1 conj?: 0 aromatic?: 0 -35: 1 1->2 order: 1 conj?: 0 aromatic?: 0 -35: 2 2->0 order: 1 conj?: 0 aromatic?: 0 -35: 3 3->4 order: 1 conj?: 0 aromatic?: 0 -35: 4 4->5 order: 1 conj?: 0 aromatic?: 0 -35: 5 5->6 order: 1 conj?: 0 aromatic?: 0 -35: 6 6->3 order: 1 conj?: 0 aromatic?: 0 -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing Issue164: Roundtrip Pickle Failure. -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing Issue219: Pickle Failure with Conformations. -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing Issue220: Pickle problems with bond stereochemistry. -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing query serialization. -35: [07:34:57] C=[$(C=O)] -35: [07:34:57] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -44: [07:34:57] WARNING: not removing hydrogen atom without neighbors -44: [07:34:57] WARNING: not removing hydrogen atom without neighbors -44: [07:34:57] Unreasonable formal charge on hydrogen # 0. -44: [07:34:57] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -44: [07:34:57] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: no atom -44: Violation occurred on line 185 in file ./Code/GraphMol/ROMol.cpp -44: Failed Expression: at -44: **** -44: -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: no owner -44: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -44: Failed Expression: dp_mol -44: **** -44: -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: atom not associated with this molecule -44: Violation occurred on line 186 in file ./Code/GraphMol/ROMol.cpp -44: Failed Expression: &at->getOwningMol() == this -44: **** -44: -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: no atom -44: Violation occurred on line 385 in file ./Code/GraphMol/ROMol.cpp -44: Failed Expression: at -44: **** -44: -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: no owner -44: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -44: Failed Expression: dp_mol -44: **** -44: -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: atom not associated with this molecule -44: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp -44: Failed Expression: &at->getOwningMol() == this -44: **** -44: -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: no atom -44: Violation occurred on line 392 in file ./Code/GraphMol/ROMol.cpp -44: Failed Expression: at -44: **** -44: -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: no owner -44: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -44: Failed Expression: dp_mol -44: **** -44: -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: atom not associated with this molecule -44: Violation occurred on line 393 in file ./Code/GraphMol/ROMol.cpp -44: Failed Expression: &at->getOwningMol() == this -44: **** -44: -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: null atom passed in -44: Violation occurred on line 407 in file ./Code/GraphMol/ROMol.cpp -44: Failed Expression: atom_pin -44: **** -44: -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: cannot take ownership of an atom which already has an owner -44: Violation occurred on line 408 in file ./Code/GraphMol/ROMol.cpp -44: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this -44: **** -44: -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: cannot take ownership of an bond which already has an owner -44: Violation occurred on line 434 in file ./Code/GraphMol/ROMol.cpp -44: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this -44: **** -44: -44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -44: [07:34:57] WARNING: not removing hydrogen atom without neighbors -44: [07:34:57] Explicit valence for atom # 1 F greater than permitted -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: plain atoms have no Query -44: Violation occurred on line 610 in file ./Code/GraphMol/Atom.cpp -44: Failed Expression: 0 -44: **** -44: -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: plain atoms have no Query -44: Violation occurred on line 615 in file ./Code/GraphMol/Atom.cpp -44: Failed Expression: 0 -44: **** -44: -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: plain bonds have no Query -44: Violation occurred on line 206 in file ./Code/GraphMol/Bond.cpp -44: Failed Expression: 0 -44: **** -44: -44: [07:34:57] -44: -44: **** -44: Pre-condition Violation -44: plain bonds have no query -44: Violation occurred on line 227 in file ./Code/GraphMol/Bond.cpp -44: Failed Expression: 0 -44: **** -44: -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -44: [07:34:57] Unusual charge on atom 0 number of radical electrons set to zero -44: [07:34:57] Unusual charge on atom 0 number of radical electrons set to zero -44: [07:34:57] Unusual charge on atom 0 number of radical electrons set to zero -44: [07:34:57] non-ring atom 0 marked aromatic -44: [07:34:57] non-ring atom 0 marked aromatic -44: [07:34:57] Explicit valence for atom # 1 C, 5, is greater than permitted -44: [07:34:57] Explicit valence for atom # 9 C, 5, is greater than permitted -44: [07:34:57] Explicit valence for atom # 3 N, 4, is greater than permitted -44: [07:34:57] Explicit valence for atom # 15 C, 5, is greater than permitted -44: [07:34:57] Explicit valence for atom # 11 C, 5, is greater than permitted -44: [07:34:57] Explicit valence for atom # 9 C, 5, is greater than permitted -44: [07:34:57] Explicit valence for atom # 9 C, 5, is greater than permitted -44: [07:34:57] Explicit valence for atom # 9 C, 6, is greater than permitted -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 7 -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 3 -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 3 7 -44: [07:34:57] Can't kekulize mol. Unkekulized atoms: 3 7 - 25/223 Test #50: moliteratorTestsCatch .................. Passed 0.05 sec -55: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -55: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -55: [07:34:57] SMILES Parse Error: syntax error while parsing: - -55: [07:34:57] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -55: [07:34:57] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -55: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -55: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -55: [07:34:57] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -55: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -55: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -55: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -55: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -55: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -55: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -55: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 26/223 Test #55: smiTest2 ............................... Passed 0.04 sec -51: Randomness seeded to: 3425740349 -51: =============================================================================== -51: All tests passed (10 assertions in 1 test case) -51: - 27/223 Test #51: queryTestsCatch ........................ Passed 0.05 sec -52: Randomness seeded to: 1569010506 -52: =============================================================================== -52: All tests passed (6 assertions in 1 test case) -52: - 28/223 Test #52: molbundleTestsCatch .................... Passed 0.05 sec -45: Randomness seeded to: 893550468 -45: =============================================================================== -45: All tests passed (62 assertions in 6 test cases) -45: - 29/223 Test #45: graphmolOrganometallicsCatch ........... Passed 0.06 sec -49: Randomness seeded to: 1172305161 -49: =============================================================================== -49: All tests passed (137 assertions in 7 test cases) -49: -53: Randomness seeded to: 297128328 -53: =============================================================================== -53: All tests passed (34 assertions in 1 test case) -53: -48: Randomness seeded to: 1002468320 -48: [07:34:57] unable to set wavy bonds for double bonds: 3 -54: [07:34:57] WARNING: not removing hydrogen atom without neighbors -54: [07:34:57] WARNING: not removing hydrogen atom without neighbors -54: [07:34:57] WARNING: not removing hydrogen atom without neighbors -54: [07:34:57] WARNING: not removing hydrogen atom without neighbors -54: [07:34:57] WARNING: not removing hydrogen atom without neighbors -54: [07:34:57] WARNING: not removing hydrogen atom without neighbors -54: [07:34:57] WARNING: not removing hydrogen atom without neighbors -54: [07:34:57] WARNING: not removing hydrogen atom without neighbors -54: [07:34:57] WARNING: not removing hydrogen atom without neighbors -54: [07:34:57] WARNING: not removing hydrogen atom without neighbors -54: [07:34:57] WARNING: not removing hydrogen atom without neighbors -54: [07:34:57] Invalid chiral specification on atom 0 -54: [07:34:57] Invalid chiral specification on atom 0 -54: [07:34:57] Invalid chiral specification on atom 0 -54: [07:34:57] Invalid chiral specification on atom 0 -54: [07:34:57] Invalid chiral specification on atom 0 2: cyclosporine a 2: RDKit 2D 2: @@ -13713,91 +13080,431 @@ 2: 30 11 1 0 2: M END 2: -33: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 -26: -26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... -47: Randomness seeded to: 1825795064 -47: =============================================================================== -47: All tests passed (281 assertions in 10 test cases) -47: -58: Randomness seeded to: 1906733627 -58: [07:34:57] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -58: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -58: [07:34:57] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -58: [07:34:57] SMARTS Parse Error: unclosed ring for input: 'C1C' -58: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -58: [07:34:57] SMARTS Parse Error: syntax error while parsing: C)foo -58: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -58: [07:34:57] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -58: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' - 30/223 Test #47: graphmolAdjustQueryCatch ............... Passed 0.07 sec - 31/223 Test #49: canonTestsCatch ........................ Passed 0.06 sec - 32/223 Test #53: pickleTestsCatch ....................... Passed 0.05 sec -test 67 - Start 67: testMultithreadedMolSupplier +30: Atoms: +30: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 0 arom?: 0 chi: 0 +30: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 +30: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 0 arom?: 0 chi: 0 +30: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 +30: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 +30: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 +30: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: 0 arom?: 0 chi: 0 +30: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: 0 arom?: 1 chi: 0 +30: 8 22 Ti chg: 0 deg: 1 exp: [04:03:45] +30: +30: **** +30: Pre-condition Violation +30: getExplicitValence() called without call to calcExplicitValence() +30: Violation occurred on line 298 in file ./Code/GraphMol/Atom.cpp +30: Failed Expression: d_explicitValence > -1 +30: **** +30: +30: N/A imp: -1 hyb: 0 arom?: 0 chi: 0 +30: Bonds: +30: 0 0->1 order: 1 conj?: 0 aromatic?: 0 +30: 1 1->2 order: 2 conj?: 0 aromatic?: 0 +30: 2 2->3 order: 1 conj?: 0 aromatic?: 0 +30: 3 0->4 order: 1 conj?: 0 aromatic?: 0 +30: 4 5->6 order: 3 conj?: 0 aromatic?: 0 +30: 5 6->7 order: 1 conj?: 0 aromatic?: 0 +30: 6 7->8 order: 2 conj?: 0 aromatic?: 0 +30: [04:03:45] +30: +30: **** +30: Pre-condition Violation +30: bond already exists +30: Violation occurred on line 380 in file ./Code/GraphMol/RWMol.cpp +30: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) +30: **** +30: +30: [04:03:45] +30: +30: **** +30: Pre-condition Violation +30: bond already exists +30: Violation occurred on line 380 in file ./Code/GraphMol/RWMol.cpp +30: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) +30: **** +30: +30: [04:03:45] +30: +30: **** +30: Pre-condition Violation +30: attempt to add self-bond +30: Violation occurred on line 379 in file ./Code/GraphMol/RWMol.cpp +30: Failed Expression: atomIdx1 != atomIdx2 +30: **** +30: +30: [04:03:45] +30: +30: **** +30: Pre-condition Violation +30: bond already exists +30: Violation occurred on line 441 in file ./Code/GraphMol/ROMol.cpp +30: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) +30: **** +30: +30: [04:03:45] +30: +30: **** +30: Pre-condition Violation +30: attempt to add self-bond +30: Violation occurred on line 439 in file ./Code/GraphMol/ROMol.cpp +30: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() +30: **** +30: +30: [04:03:45] Explicit valence for atom # 0 B, 4, is greater than permitted +30: [04:03:45] Explicit valence for atom # 0 B, 5, is greater than permitted +31: +31: +31: +31: COPY +32: [04:03:45] ---------------------- Test1 + 15/223 Test #2: testCoordGen ........................... Passed 0.42 sec + 16/223 Test #28: testDistGeom ........................... Passed 0.15 sec + 17/223 Test #31: graphmolcpTest ......................... Passed 0.08 sec +test 35 + Start 35: graphmoltestPickler -67: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier -67: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -67: Test timeout computed to be: 1500 -test 68 - Start 68: testMolWriter +35: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPickler +35: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +35: Test timeout computed to be: 1500 +test 36 + Start 36: graphmoltestPicklerGlobalSetting -68: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter -68: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -68: Test timeout computed to be: 1500 -test 69 - Start 69: testTplParser +36: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting +36: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +36: Test timeout computed to be: 1500 +test 37 + Start 37: graphmolIterTest -69: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser -69: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -69: Test timeout computed to be: 1500 -test 70 - Start 70: testMol2ToMol +37: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolIterTest +37: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +37: Test timeout computed to be: 1500 +3: .... +3: ---------------------------------------------------------------------- +3: Ran 4 tests in 0.040s +3: +3: OK +30: [04:03:45] +30: +30: **** +30: Post-condition Violation +30: Element 'Xx' not found +30: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +30: Failed Expression: anum > -1 +30: **** +30: +30: [04:03:45] ------------------------------------- +30: [04:03:45] Test github381: thread-safe initialization of the periodic table +32: [04:03:45] Done! +32: [04:03:45] ---------------------- Test2 +32: [04:03:45] Done! +32: [04:03:45] ---------------------- Test3 +32: [04:03:45] Done! +32: [04:03:45] ---------------------- Test4 +32: [04:03:45] Done! +32: [04:03:45] ---------------------- Test5 +32: [04:03:45] Done! +32: [04:03:45] Done! +32: [04:03:45] ---------------------- Test issue 2892580 +32: [04:03:45] Done! +32: [04:03:45] ---------------------- Test github issue 53: query molecules not matching [R] +32: [04:03:45] Done! +32: [04:03:45] ---------------------- Test queries using qualifiers instead of == +32: [04:03:45] Done! +32: [04:03:45] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +32: [04:03:45] Done! +32: [04:03:45] ---------------------- Test extra atom queries +32: [04:03:45] Done! +32: [04:03:45] ---------------------- Test extra bond queries +32: [04:03:45] Done! +32: [04:03:45] ---------------------- Test num heteroatom neighbor queries +32: [04:03:45] Done! +32: [04:03:45] ---------------------- Test atom type queries +32: [04:03:45] Done! +32: [04:03:45] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +32: [04:03:45] Done! +32: [04:03:45] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +32: [04:03:45] Done! +25: done +25: ------------------------------------- +25: Unit tests for copying UFF ForceFields. +35: [04:03:45] ------------------------------------- +35: [04:03:45] Testing String Pickle Roundtrips. + 18/223 Test #32: graphmolqueryTest ...................... Passed 0.12 sec +test 38 + Start 38: hanoiTest -70: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol -70: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -70: Test timeout computed to be: 1500 -test 71 - Start 71: testSequence +38: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest +38: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +38: Test timeout computed to be: 1500 +14: ......... +14: ---------------------------------------------------------------------- +14: Ran 9 tests in 0.011s +14: +14: OK +34: -------------------------- +34: -------------------------- +34: C/C=C/C(C)Cl +25: done +25: ------------------------------------- +25: Unit test for UFF butane scan. +36: [04:03:45] done + 19/223 Test #36: graphmoltestPicklerGlobalSetting ....... Passed 0.07 sec +test 39 + Start 39: graphmolMemTest1 -71: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence -71: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -71: Test timeout computed to be: 1500 -test 72 - Start 72: testExtendedStereoParsing +39: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 +39: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +39: Test timeout computed to be: 1500 +15: ......... +15: ---------------------------------------------------------------------- +15: Ran 9 tests in 0.054s +15: +15: OK +34: [04:03:45] Conflicting single bond directions around double bond at index 2. +34: [04:03:45] BondStereo set to STEREONONE and single bond directions set to NONE. +34: [04:03:45] Conflicting single bond directions around double bond at index 4. +34: [04:03:45] BondStereo set to STEREONONE and single bond directions set to NONE. +34: [04:03:45] Conflicting single bond directions around double bond at index 15. +34: [04:03:45] BondStereo set to STEREONONE and single bond directions set to NONE. +34: [04:03:45] Conflicting single bond directions around double bond at index 2. +34: [04:03:45] BondStereo set to STEREONONE and single bond directions set to NONE. +34: [04:03:45] Conflicting single bond directions around double bond at index 1. +34: [04:03:45] BondStereo set to STEREONONE and single bond directions set to NONE. + 20/223 Test #37: graphmolIterTest ....................... Passed 0.08 sec +test 40 + Start 40: resMolSupplierTest -72: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing -72: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -72: Test timeout computed to be: 1500 -test 73 - Start 73: fileParsersCatchTest +40: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest +40: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +40: Test timeout computed to be: 1500 +33: 1 1 2 +33: 1 1 1 +33: 2 1 0.75 +33: path: 2 +33: [04:03:45] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +33: [04:03:45] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 13 ignored +33: [04:03:45] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +30: [04:03:45] done +30: [04:03:45] ------------------------------------- +30: [04:03:45] Test github1041: Segfault for atom with no owner (expect some warnings) +30: [04:03:45] +30: +30: **** +30: Pre-condition Violation +30: no owner +30: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +30: Failed Expression: dp_mol +30: **** +30: +30: [04:03:45] +30: +30: **** +30: Pre-condition Violation +30: no owner +30: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h +30: Failed Expression: dp_mol +30: **** +30: +30: [04:03:45] done +30: [04:03:45] ------------------------------------- +30: [04:03:45] Test github1041: Segfault for atom with no owner (expect some warnings) +30: [04:03:45] +30: +30: **** +30: Pre-condition Violation +30: no owner +30: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +30: Failed Expression: dp_mol +30: **** +30: +30: [04:03:45] +30: +30: **** +30: Pre-condition Violation +30: no owner +30: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h +30: Failed Expression: dp_mol +30: **** +30: +30: [04:03:45] done +30: [04:03:45] ------------------------------------- +30: [04:03:45] Test github1453: RWMol.clear() should reset the numBonds count. +30: [04:03:45] done +30: [04:03:45] ------------------------------------- +30: [04:03:45] Test range-based for loops. +30: [04:03:45] done +30: [04:03:45] ------------------------------------- +30: [04:03:45] Test github1642: Atom index type is too low for big molecules. + 21/223 Test #3: pyCoordGen ............................. Passed 0.55 sec + 22/223 Test #39: graphmolMemTest1 ....................... Passed 0.05 sec +test 41 + Start 41: molBundleTest -73: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -73: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -73: Test timeout computed to be: 1500 -test 74 - Start 74: testPropertyLists +41: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/molBundleTest +41: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +41: Test timeout computed to be: 1500 +test 42 + Start 42: testSGroup -74: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists -74: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -74: Test timeout computed to be: 1500 -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing radical handling in pickles. -35: [07:34:57] done -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing sf.net issue 2788233. -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing sf.net issue 3202580. +42: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/testSGroup +42: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +42: Test timeout computed to be: 1500 +33: [04:03:45] Explicit valence for atom # 0 B, 5, is greater than permitted +33: [04:03:45] Explicit valence for atom # 1 C, 5, is greater than permitted +33: [04:03:45] Explicit valence for atom # 1 C, 5, is greater than permitted +33: [04:03:45] Explicit valence for atom # 1 C, 5, is greater than permitted +33: [04:03:45] Explicit valence for atom # 1 Si, 7, is greater than permitted +34: -------------------------------------------------- + 23/223 Test #34: graphmoltestChirality .................. Passed 0.20 sec +test 43 + Start 43: test-valgrind + +43: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/test-valgrind +43: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +43: Test timeout computed to be: 1500 +35: [04:03:45] done +35: [04:03:45] ------------------------------------- +35: [04:03:45] Testing reading existing pickle file (v2). +4: dynamic boost any:0.43284 s + 24/223 Test #14: pySparseIntVect ........................ Passed 0.54 sec +test 44 + Start 44: graphmolTestsCatch + +44: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +44: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +44: Test timeout computed to be: 1500 +26: +26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... + 25/223 Test #41: molBundleTest .......................... Passed 0.07 sec +test 45 + Start 45: graphmolOrganometallicsCatch + +45: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch +45: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +45: Test timeout computed to be: 1500 + 26/223 Test #43: test-valgrind .......................... Passed 0.06 sec +test 46 + Start 46: graphmolSGroupCatch + +46: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolSGroupCatch +46: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +46: Test timeout computed to be: 1500 +23: ..... +23: ---------------------------------------------------------------------- +23: Ran 5 tests in 0.002s +23: +23: OK +23: Testing Alignment Wrapper code: + 27/223 Test #42: testSGroup ............................. Passed 0.10 sec +test 47 + Start 47: graphmolAdjustQueryCatch + +47: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch +47: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +47: Test timeout computed to be: 1500 +35: [04:03:45] done +35: [04:03:45] ------------------------------------- +35: [04:03:45] Testing combining molecules using pickles. +35: Atoms: +35: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 +35: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 +35: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 +35: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 +35: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 +35: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 4 arom?: 0 chi: 0 +35: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 +35: Bonds: +35: 0 0->1 order: 1 conj?: 0 aromatic?: 0 +35: 1 1->2 order: 1 conj?: 0 aromatic?: 0 +35: 2 2->0 order: 1 conj?: 0 aromatic?: 0 +35: 3 3->4 order: 1 conj?: 0 aromatic?: 0 +35: 4 4->5 order: 1 conj?: 0 aromatic?: 0 +35: 5 5->6 order: 1 conj?: 0 aromatic?: 0 +35: 6 6->3 order: 1 conj?: 0 aromatic?: 0 +35: [04:03:45] done +35: [04:03:45] ------------------------------------- +35: [04:03:45] Testing Issue164: Roundtrip Pickle Failure. +44: Randomness seeded to: 3975322502 +44: [04:03:45] WARNING: not removing hydrogen atom without neighbors +44: [04:03:45] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +44: [04:03:45] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +44: [04:03:45] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +44: [04:03:45] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +4: static RDAny:0.066813 s +46: Randomness seeded to: 1189005469 +46: =============================================================================== +46: All tests passed (120 assertions in 6 test cases) +46: + 28/223 Test #46: graphmolSGroupCatch .................... Passed 0.06 sec +test 48 + Start 48: chiralityTestsCatch + +48: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/chiralityTestsCatch +48: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +48: Test timeout computed to be: 1500 +44: [04:03:45] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +44: [04:03:45] Explicit valence for atom # 1 N, 5, is greater than permitted +44: [04:03:45] Explicit valence for atom # 1 N, 6, is greater than permitted +44: [04:03:45] Explicit valence for atom # 1 N, 5, is greater than permitted +44: [04:03:45] Explicit valence for atom # 1 N, 5, is greater than permitted +44: [04:03:45] Explicit valence for atom # 2 O, 3, is greater than permitted +44: [04:03:45] Explicit valence for atom # 2 O, 3, is greater than permitted +44: [04:03:45] non-ring atom 2 marked aromatic +44: [04:03:45] non-ring atom 2 marked aromatic +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 1 2 3 +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 1 2 3 +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 0 1 2 +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 0 1 2 +44: [04:03:45] Explicit valence for atom # 1 O, 3, is greater than permitted +44: [04:03:45] Explicit valence for atom # 4 F, 2, is greater than permitted +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 6 7 8 +44: [04:03:45] Explicit valence for atom # 1 C, 5, is greater than permitted +44: [04:03:45] WARNING: not removing hydrogen atom with dummy atom neighbors +44: [04:03:45] WARNING: not removing hydrogen atom with dummy atom neighbors +44: [04:03:45] WARNING: not removing hydrogen atom with wedged bond +44: [04:03:45] WARNING: not removing hydrogen atom without neighbors +44: [04:03:45] WARNING: not removing hydrogen atom without neighbors +35: [04:03:45] done +35: [04:03:45] ------------------------------------- +35: [04:03:45] Testing Issue219: Pickle Failure with Conformations. +35: [04:03:45] done +35: [04:03:45] ------------------------------------- +35: [04:03:45] Testing Issue220: Pickle problems with bond stereochemistry. +35: [04:03:45] done +35: [04:03:45] ------------------------------------- +35: [04:03:45] Testing query serialization. +35: [04:03:45] C=[$(C=O)] +35: [04:03:45] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +35: [04:03:45] done +35: [04:03:45] ------------------------------------- +35: [04:03:45] Testing radical handling in pickles. +35: [04:03:45] done +35: [04:03:45] done +35: [04:03:45] ------------------------------------- +35: [04:03:45] Testing sf.net issue 2788233. +35: [04:03:45] done +35: [04:03:45] ------------------------------------- +35: [04:03:45] Testing sf.net issue 3202580. 35: mass! 13.0034 -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing sf.net issue 3316407. -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing sf.net issue 3496759. +35: [04:03:45] done +35: [04:03:45] ------------------------------------- +35: [04:03:45] Testing sf.net issue 3316407. +35: [04:03:45] done +35: [04:03:45] ------------------------------------- +35: [04:03:45] Testing sf.net issue 3496759. +19: ........... +19: ---------------------------------------------------------------------- +19: Ran 11 tests in 0.068s +19: +19: OK +19: Testing Geometry wrapper +44: [04:03:45] WARNING: not removing hydrogen atom without neighbors +44: [04:03:45] WARNING: not removing hydrogen atom without neighbors +44: [04:03:45] Unreasonable formal charge on hydrogen # 0. 35: smi match: *C *C 35: smi match: **=* **=* 35: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O @@ -13811,6 +13518,7 @@ 35: smi match: *=C=N *=C=N 35: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F 35: smi match: SP(S)=S SP(S)=S +33: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 35: smi match: NP(N)(N)=O NP(N)(N)=O 35: smi match: cN=[N+]=[N-] cN=[N+]=[N-] 35: smi match: *CC=O *CC=O @@ -13828,6 +13536,161 @@ 35: smi match: N#CS(=O)=O N#CS(=O)=O 35: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC 35: smi match: N#CN=N N#CN=N +44: [04:03:45] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +44: [04:03:45] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: no atom +44: Violation occurred on line 185 in file ./Code/GraphMol/ROMol.cpp +44: Failed Expression: at +44: **** +44: +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: no owner +44: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +44: Failed Expression: dp_mol +44: **** +44: +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: atom not associated with this molecule +44: Violation occurred on line 186 in file ./Code/GraphMol/ROMol.cpp +44: Failed Expression: &at->getOwningMol() == this +44: **** +44: +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: no atom +44: Violation occurred on line 385 in file ./Code/GraphMol/ROMol.cpp +44: Failed Expression: at +44: **** +44: +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: no owner +44: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +44: Failed Expression: dp_mol +44: **** +44: +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: atom not associated with this molecule +44: Violation occurred on line 386 in file ./Code/GraphMol/ROMol.cpp +44: Failed Expression: &at->getOwningMol() == this +44: **** +44: +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: no atom +44: Violation occurred on line 392 in file ./Code/GraphMol/ROMol.cpp +44: Failed Expression: at +44: **** +44: +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: no owner +44: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +44: Failed Expression: dp_mol +44: **** +44: +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: atom not associated with this molecule +44: Violation occurred on line 393 in file ./Code/GraphMol/ROMol.cpp +44: Failed Expression: &at->getOwningMol() == this +44: **** +44: +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: null atom passed in +44: Violation occurred on line 407 in file ./Code/GraphMol/ROMol.cpp +44: Failed Expression: atom_pin +44: **** +44: +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: cannot take ownership of an atom which already has an owner +44: Violation occurred on line 408 in file ./Code/GraphMol/ROMol.cpp +44: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this +44: **** +44: +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: cannot take ownership of an bond which already has an owner +44: Violation occurred on line 434 in file ./Code/GraphMol/ROMol.cpp +44: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this +44: **** +44: +44: [04:03:45] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +44: [04:03:45] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +44: [04:03:45] WARNING: not removing hydrogen atom without neighbors +44: [04:03:45] Explicit valence for atom # 1 F greater than permitted +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: plain atoms have no Query +44: Violation occurred on line 610 in file ./Code/GraphMol/Atom.cpp +44: Failed Expression: 0 +44: **** +44: +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: plain atoms have no Query +44: Violation occurred on line 615 in file ./Code/GraphMol/Atom.cpp +44: Failed Expression: 0 +44: **** +44: +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: plain bonds have no Query +44: Violation occurred on line 206 in file ./Code/GraphMol/Bond.cpp +44: Failed Expression: 0 +44: **** +44: +44: [04:03:45] +44: +44: **** +44: Pre-condition Violation +44: plain bonds have no query +44: Violation occurred on line 227 in file ./Code/GraphMol/Bond.cpp +44: Failed Expression: 0 +44: **** +44: +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 35: smi match: N=NCC=O N=NCC=O 35: smi match: CCCCCCC CCCCCCC 35: smi match: OCCOCCO OCCOCCO @@ -13851,7 +13714,19 @@ 35: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 35: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 35: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 +44: [04:03:45] Unusual charge on atom 0 number of radical electrons set to zero +44: [04:03:45] Unusual charge on atom 0 number of radical electrons set to zero +44: [04:03:45] Unusual charge on atom 0 number of radical electrons set to zero +44: [04:03:45] non-ring atom 0 marked aromatic +44: [04:03:45] non-ring atom 0 marked aromatic 35: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 + 29/223 Test #15: pyFPB .................................. Passed 0.69 sec +test 49 + Start 49: canonTestsCatch + +49: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/canonTestsCatch +49: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +49: Test timeout computed to be: 1500 35: smi match: cN(=O)~O cN(=O)~O 35: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O 35: smi match: N~NC=O N~NC=O @@ -13986,6 +13861,30 @@ 35: smi match: SC(S)=C(S)S SC(S)=C(S)S 35: smi match: N=CC=NO N=CC=NO 35: smi match: N#CCC#N N#CCC#N +29: ...... +29: ---------------------------------------------------------------------- +29: Ran 6 tests in 0.002s +29: +29: OK +44: [04:03:45] Explicit valence for atom # 1 C, 5, is greater than permitted +44: [04:03:45] Explicit valence for atom # 9 C, 5, is greater than permitted +44: [04:03:45] Explicit valence for atom # 3 N, 4, is greater than permitted +44: [04:03:45] Explicit valence for atom # 15 C, 5, is greater than permitted +44: [04:03:45] Explicit valence for atom # 11 C, 5, is greater than permitted +44: [04:03:45] Explicit valence for atom # 9 C, 5, is greater than permitted +44: [04:03:45] Explicit valence for atom # 9 C, 5, is greater than permitted +44: [04:03:45] Explicit valence for atom # 9 C, 6, is greater than permitted +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 7 +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 3 +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 3 7 +44: [04:03:45] Can't kekulize mol. Unkekulized atoms: 3 7 +44: [04:03:45] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +13: ...... +13: ---------------------------------------------------------------------- +13: Ran 6 tests in 0.003s +13: +13: OK 35: smi match: CON=O CON=O 35: smi match: C=CN C=CN 35: smi match: C=N[SH](=O)=O C=N[SH](=O)=O @@ -13997,104 +13896,6 @@ 35: smi match: C1COCO1 C1COCO1 35: smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O 35: smi match: O=CC=O O=CC=O -44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -44: [07:34:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -48: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -48: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -48: [07:34:57] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -48: [07:34:57] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -48: [07:34:57] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored -48: [07:34:57] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored -48: [07:34:57] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored -48: =============================================================================== -48: All tests passed (1845 assertions in 63 test cases) -48: -54: [07:34:57] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -54: [07:34:57] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -33: [07:34:57] non-ring atom 0 marked aromatic -33: [07:34:57] non-ring atom 0 marked aromatic -33: [07:34:57] Conflicting single bond directions around double bond at index 17. -33: [07:34:57] BondStereo set to STEREONONE and single bond directions set to NONE. -33: starting ring finding -33: done -33: starting ring finding -33: done -33: starting ring finding -33: done -33: 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 -33: starting sanitization -33: done -33: starting sanitization -58: [07:34:57] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -59: Randomness seeded to: 69754176 -59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [07:34:57] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [07:34:57] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -59: =============================================================================== -59: All tests passed (308 assertions in 9 test cases) -59: -65: [07:34:57] -65: ----------------------------------------- -65: [07:34:57] -65: -65: **** -65: Invariant Violation -65: bad prop value -65: Violation occurred on line 158 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -65: Failed Expression: nSwaps < 2 -65: **** -65: -66: [07:34:57] -66: ----------------------------------------- -66: [07:34:57] Finished: testDetermineFormat() -66: [07:34:57] ----------------------------------------- -66: -66: [07:34:57] -66: ----------------------------------------- -66: [07:34:57] Finished: testSdf() -66: [07:34:57] ----------------------------------------- -66: -66: [07:34:57] -66: ----------------------------------------- -66: [07:34:57] Finished: testSmi() -66: [07:34:57] ----------------------------------------- -66: -66: [07:34:57] -66: ----------------------------------------- -64: *************************************** -64: *************************************** -64: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -64: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -64: [07:34:57] bond with order 0 found on line 7. This is not part of the MDL specification. -67: [07:34:57] -67: ----------------------------------------- - 33/223 Test #2: testCoordGen ........................... Passed 0.21 sec - 34/223 Test #48: chiralityTestsCatch .................... Passed 0.11 sec - 35/223 Test #59: nontetrahedralCatch .................... Passed 0.07 sec -test 75 - Start 75: XYZFileParserCatchTest - -75: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest -75: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -75: Test timeout computed to be: 1500 -test 76 - Start 76: cdxmlParserCatchTest - -76: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest -76: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -76: Test timeout computed to be: 1500 -test 77 - Start 77: molfileStereoCatchTest - -77: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest -77: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -77: Test timeout computed to be: 1500 35: smi match: O=CNOC=O O=CNOC=O 35: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 35: smi match: ONO ONO @@ -14119,7 +13920,18 @@ 35: smi match: OOO OOO 35: smi match: OO OO 35: smi match: O~Cl(~O)~O O~Cl(~O)~O +45: Randomness seeded to: 903818387 +45: =============================================================================== +45: All tests passed (62 assertions in 6 test cases) +45: 35: smi match: O~Cl(~O)(~O)~O O~Cl(~O)(~O)~O + 30/223 Test #45: graphmolOrganometallicsCatch ........... Passed 0.17 sec +test 50 + Start 50: moliteratorTestsCatch + +50: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/moliteratorTestsCatch +50: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +50: Test timeout computed to be: 1500 35: smi match: [OH]~C(~O)~O [OH]~C(~O)~O 35: smi match: *N *N 35: smi match: *P *P @@ -14161,21 +13973,666 @@ 35: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O 35: smi match: *C[SH](=O)=O *C[SH](=O)=O 35: smi match: * * -44: [07:34:57] Explicit valence for atom # 1 O, 3, is greater than permitted -44: [07:34:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -44: [07:34:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -44: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -44: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +35: smi match: *1CC1 *1CC1 +35: smi match: O=COC=O O=COC=O +35: smi match: N=C=O N=C=O +35: smi match: N=C=S N=C=S +35: smi match: O~O O~O +35: smi match: N~[SiH4] N~[SiH4] +35: smi match: *P *P +35: smi match: C=N=N C=N=N +35: smi match: *N#[NH+] *N#[NH+] +35: smi match: *S* *S* +35: smi match: ** ** +35: smi match: *CC* *CC* +35: smi match: *O[SiH3] *O[SiH3] +35: smi match: *OS(*)~O *OS(*)~O +35: smi match: N~N~O N~N~O +35: smi match: *N(~O)(~O)~O *N(~O)(~O)~O +35: smi match: *[N+](=C)[O-] *[N+](=C)[O-] +35: smi match: * * +35: smi match: *C(*)NCN(*)* *C(*)NCN(*)* +35: smi match: *OCC#N *OCC#N +35: smi match: **C=C **C=C +35: smi match: C=C[O-] C=C[O-] +35: smi match: C=CO C=CO +35: smi match: * * +35: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O +35: smi match: O=COn1ccnc1 O=COn1ccnc1 +35: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F +35: smi match: CC(C)(C)S CC(C)(C)S +35: 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 +33: [04:03:45] non-ring atom 0 marked aromatic +33: [04:03:45] non-ring atom 0 marked aromatic +47: Randomness seeded to: 558354295 +47: =============================================================================== +47: All tests passed (281 assertions in 10 test cases) +47: +44: [04:03:45] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. + 31/223 Test #47: graphmolAdjustQueryCatch ............... Passed 0.14 sec +test 51 + Start 51: queryTestsCatch + +51: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/queryTestsCatch +51: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +51: Test timeout computed to be: 1500 +35: smi match: [CH]=O [CH]=O +35: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C +35: smi match: SS SS +35: smi match: [SH] [SH] +35: smi match: *C* *C* +35: smi match: * * +35: smi match: C[nH3+] C[nH3+] +35: smi match: cC(=N)[NH2] cC(=N)[NH2] +35: smi match: O=CN[OH] O=CN[OH] +35: smi match: NN NN +35: smi match: * * +35: smi match: *OP(=O)O* *OP(=O)O* +35: smi match: * * +35: smi match: * * +35: smi match: * * +35: smi match: *N=C(*)* *N=C(*)* +35: smi match: *C(*)(*)C=O *C(*)(*)C=O +35: smi match: CSC=O CSC=O +35: smi match: * * +35: smi match: O=CCl O=CCl +35: smi match: *** *** +35: smi match: *C=O *C=O +35: smi match: C[OH] C[OH] +35: smi match: C[OH] C[OH] +35: smi match: C[OH] C[OH] +35: smi match: C[OH] C[OH] +35: smi match: C[CH]=O C[CH]=O +35: smi match: *=* *=* +35: smi match: *C *C +35: smi match: C#C C#C +35: smi match: *[CH]C=C *[CH]C=C +35: smi match: cCC(=O)[OH] cCC(=O)[OH] +35: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] +35: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] +35: smi match: C=CC(=O)[OH] C=CC(=O)[OH] +35: smi match: N#CC(=O)[OH] N#CC(=O)[OH] +35: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O +35: smi match: *N(*)C*=O *N(*)C*=O +33: [04:03:45] Conflicting single bond directions around double bond at index 17. +33: [04:03:45] BondStereo set to STEREONONE and single bond directions set to NONE. +33: starting ring finding +33: done +33: starting ring finding +48: Randomness seeded to: 3670173800 +48: [04:03:45] unable to set wavy bonds for double bonds: 3 + 32/223 Test #19: testPyGeometry ......................... Passed 0.70 sec +test 52 + Start 52: molbundleTestsCatch + +52: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/molbundleTestsCatch +52: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +52: Test timeout computed to be: 1500 +35: smi match: O=*C[OH] O=*C[OH] +35: smi match: *=C*=O *=C*=O +35: smi match: *=CC#N *=CC#N +35: smi match: *C[OH] *C[OH] +35: smi match: ** ** +35: smi match: *C[OH] *C[OH] +35: smi match: *C(*)=O *C(*)=O +35: smi match: * * +35: smi match: *CC(=O)[OH] *CC(=O)[OH] +35: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O +35: smi match: *c *c +35: smi match: CN(C)c CN(C)c +35: smi match: c c +35: smi match: *c *c +35: smi match: *c *c +35: smi match: **:*cF **:*cF +35: smi match: cB([OH])[OH] cB([OH])[OH] +35: smi match: N~N~N N~N~N +35: smi match: *N=N* *N=N* +35: smi match: *CC[OH] *CC[OH] +35: smi match: *CC[OH] *CC[OH] +35: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] +35: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] +35: smi match: *CCC(=O)[OH] *CCC(=O)[OH] +35: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] +35: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O +35: smi match: *OC(*)=O *OC(*)=O +35: smi match: *C(=O)[OH] *C(=O)[OH] +35: smi match: O=C[OH] O=C[OH] +35: smi match: *OC(=O)O* *OC(=O)O* +35: smi match: * * +35: smi match: *OC(=O)Cl *OC(=O)Cl +35: smi match: *C#N *C#N +35: smi match: NCC(=O)NCC=O NCC(=O)NCC=O +35: smi match: SS SS +35: smi match: * * +35: smi match: *=* *=* +35: smi match: *=* *=* +35: smi match: *=* *=* +35: smi match: *=* *=* +35: smi match: C1CO1 C1CO1 +35: smi match: *OC(*)=O *OC(*)=O +35: smi match: * * +35: smi match: *O*[OH] *O*[OH] +35: smi match: COC(C)(C)O COC(C)(C)O +35: smi match: *[OH] *[OH] +35: smi match: ** ** +35: smi match: C=N[NH2] C=N[NH2] +35: smi match: C=NC=O C=NC=O +35: smi match: * * +35: smi match: C#NC C#NC +35: smi match: CN=C=O CN=C=O +35: smi match: CN=C=S CN=C=S +35: smi match: *OC(*)(*)O* *OC(*)(*)O* +35: smi match: *C(*)=O *C(*)=O +35: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C +35: smi match: *~*=O *~*=O +35: smi match: *~*=O *~*=O +35: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] +35: smi match: * * +35: smi match: *C#N *C#N +35: smi match: *N(=O)~O *N(=O)~O +35: smi match: N N +35: smi match: OC(=O)C(O)=O OC(=O)C(O)=O +35: smi match: C=NO C=NO +35: smi match: O~O O~O +35: smi match: c[OH] c[OH] +35: smi match: O=P(~[OH])~O O=P(~[OH])~O +35: smi match: CO~P(=O)~O CO~P(=O)~O +35: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O +35: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O +35: smi match: O=P(~O)~O O=P(~O)~O +35: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O +35: smi match: C[NH2] C[NH2] +35: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 +35: smi match: * * +35: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 +35: smi match: CS(C)~O CS(C)~O +35: smi match: CS(C)(~O)~O CS(C)(~O)~O +35: smi match: CS(N)(~O)~O CS(N)(~O)~O +35: smi match: CS([OH])(~O)~O CS([OH])(~O)~O +35: smi match: COS(C)(~O)~O COS(C)(~O)~O +35: smi match: *S(C)(~O)~O *S(C)(~O)~O +35: smi match: CN(C)C CN(C)C +35: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 +35: smi match: *C(*)=S *C(*)=S +33: done +33: starting ring finding +33: done +33: 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 +33: starting sanitization +48: [04:03:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +48: [04:03:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +44: [04:03:46] Explicit valence for atom # 1 O, 3, is greater than permitted +44: [04:03:46] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +44: [04:03:46] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +44: [04:03:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +44: [04:03:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 44: =============================================================================== 44: All tests passed (1630 assertions in 89 test cases) 44: +49: Randomness seeded to: 2239139572 +49: =============================================================================== +49: All tests passed (137 assertions in 7 test cases) +49: +50: Randomness seeded to: 804233468 +50: =============================================================================== +50: All tests passed (14 assertions in 4 test cases) +50: + 33/223 Test #23: pyAlignment ............................ Passed 0.68 sec + 34/223 Test #29: pyDistGeom ............................. Passed 0.59 sec +test 53 + Start 53: pickleTestsCatch + +53: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/pickleTestsCatch +53: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol +53: Test timeout computed to be: 1500 +test 54 + Start 54: smiTest1 + +54: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 +54: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +54: Test timeout computed to be: 1500 +35: smi match: *OC(*)=S *OC(*)=S +35: smi match: * * +35: smi match: C[SH] C[SH] +35: smi match: c[SH] c[SH] +35: smi match: NC(N)=S NC(N)=S +35: smi match: * * +35: smi match: ***** ***** +35: smi match: NC(N)=O NC(N)=O +35: [04:03:46] done +35: [04:03:46] ------------------------------------- +35: [04:03:46] Testing sf.net issue 280. +35: [04:03:46] done +35: [04:03:46] ------------------------------------- +35: [04:03:46] Testing sf.net issue 285. +35: [04:03:46] done +35: [04:03:46] done +35: [04:03:46] done +35: [04:03:46] done +35: [04:03:46] done +35: [04:03:46] done +35: [04:03:46] done +35: [04:03:46] ------------------------------------- +35: [04:03:46] Testing Github2441: Add RDProps interface to Conformers. +35: [04:03:46] done +35: [04:03:46] ------------------------------------- +35: [04:03:46] Testing Issue2510: Pickle Confs as double. +35: [04:03:46] done +35: [04:03:46] ------------------------------------- +35: [04:03:46] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +35: [04:03:46] done +35: [04:03:46] ------------------------------------- +35: [04:03:46] Testing loading pickled mols with conformers +35: [04:03:46] done +35: [04:03:46] ------------------------------------- +35: [04:03:46] Testing conformer reading/writing options +35: [04:03:46] done +35: [04:03:46] ------------------------------------- +35: [04:03:46] Testing property reading options +35: [04:03:46] done +35: [04:03:46] ------------------------------------- +35: [04:03:46] Testing property reading options +35: [04:03:46] done +35: [04:03:46] ------------------------------------- +35: [04:03:46] Testing boost::serialization integration +35: [04:03:46] done +35: [04:03:46] ------------------------------------- +35: [04:03:46] Testing github issue 6036 +33: done + 35/223 Test #44: graphmolTestsCatch ..................... Passed 0.28 sec + 36/223 Test #50: moliteratorTestsCatch .................. Passed 0.09 sec +51: Randomness seeded to: 462407685 +51: =============================================================================== +51: All tests passed (10 assertions in 1 test case) +51: + 37/223 Test #35: graphmoltestPickler .................... Passed 0.47 sec + 38/223 Test #49: canonTestsCatch ........................ Passed 0.12 sec + 39/223 Test #51: queryTestsCatch ........................ Passed 0.07 sec +test 55 + Start 55: smiTest2 + +55: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 +55: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +55: Test timeout computed to be: 1500 +test 56 + Start 56: cxsmilesTest + +56: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest +56: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +56: Test timeout computed to be: 1500 +test 57 + Start 57: smaTest1 + +57: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 +57: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +57: Test timeout computed to be: 1500 +test 58 + Start 58: smiTestCatch + +58: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +58: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +58: Test timeout computed to be: 1500 +test 59 + Start 59: nontetrahedralCatch + +59: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch +59: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +59: Test timeout computed to be: 1500 +33: starting sanitization 33: done 33: starting ring finding 33: done 33: starting ring finding 33: done 33: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 - 36/223 Test #69: testTplParser .......................... Passed 0.05 sec +33: [04:03:46] WARNING: not removing hydrogen atom with dummy atom neighbors +33: ------------------------------- +33: [04:03:46] Explicit valence for atom # 0 N, 4, is greater than permitted +33: [04:03:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +33: [04:03:46] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +33: [04:03:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +33: [04:03:46] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +52: Randomness seeded to: 3808484225 +52: =============================================================================== +52: All tests passed (6 assertions in 1 test case) +52: +53: Randomness seeded to: 1226064961 +53: =============================================================================== +53: All tests passed (34 assertions in 1 test case) +53: +48: [04:03:46] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +48: [04:03:46] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +48: [04:03:46] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored +48: [04:03:46] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored +48: [04:03:46] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +48: =============================================================================== +48: All tests passed (1845 assertions in 63 test cases) +48: +54: [04:03:46] WARNING: not removing hydrogen atom without neighbors +54: [04:03:46] WARNING: not removing hydrogen atom without neighbors +54: [04:03:46] WARNING: not removing hydrogen atom without neighbors +54: [04:03:46] WARNING: not removing hydrogen atom without neighbors +54: [04:03:46] WARNING: not removing hydrogen atom without neighbors +54: [04:03:46] WARNING: not removing hydrogen atom without neighbors +54: [04:03:46] WARNING: not removing hydrogen atom without neighbors +54: [04:03:46] WARNING: not removing hydrogen atom without neighbors +54: [04:03:46] WARNING: not removing hydrogen atom without neighbors +54: [04:03:46] WARNING: not removing hydrogen atom without neighbors +54: [04:03:46] WARNING: not removing hydrogen atom without neighbors +54: [04:03:46] Invalid chiral specification on atom 0 +54: [04:03:46] Invalid chiral specification on atom 0 +55: [04:03:46] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +55: [04:03:46] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +55: [04:03:46] SMILES Parse Error: syntax error while parsing: - +55: [04:03:46] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +55: [04:03:46] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +55: [04:03:46] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +55: [04:03:46] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +55: [04:03:46] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +55: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +55: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +55: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +55: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +55: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +55: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +55: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 40/223 Test #48: chiralityTestsCatch .................... Passed 0.25 sec + 41/223 Test #52: molbundleTestsCatch .................... Passed 0.12 sec + 42/223 Test #53: pickleTestsCatch ....................... Passed 0.09 sec + 43/223 Test #55: smiTest2 ............................... Passed 0.07 sec +test 60 + Start 60: testDepictor + +60: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor +60: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor +60: Test timeout computed to be: 1500 +test 61 + Start 61: depictorCatch + +61: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch +61: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor +61: Test timeout computed to be: 1500 +test 62 + Start 62: pyDepictor + +62: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap/testDepictor.py" +62: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap +62: Test timeout computed to be: 1500 +test 63 + Start 63: testMrvToMol + +63: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +63: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MarvinParse +63: Test timeout computed to be: 1500 +33: [04:03:46] WARNING: not removing hydrogen atom with dummy atom neighbors +54: [04:03:46] Invalid chiral specification on atom 0 +54: [04:03:46] Invalid chiral specification on atom 0 +54: [04:03:46] Invalid chiral specification on atom 0 +54: [04:03:46] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +54: [04:03:46] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +25: done +58: Randomness seeded to: 1736596335 +58: [04:03:46] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +58: [04:03:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +58: [04:03:46] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +58: [04:03:46] SMARTS Parse Error: unclosed ring for input: 'C1C' +58: [04:03:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +58: [04:03:46] SMARTS Parse Error: syntax error while parsing: C)foo +58: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +58: [04:03:46] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +58: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +58: [04:03:46] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +59: Randomness seeded to: 1169885977 +59: [04:03:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry + 44/223 Test #13: pyDiscreteValueVect .................... Passed 0.96 sec + 45/223 Test #25: testUFFForceField ...................... Passed 0.81 sec +test 64 + Start 64: fileParsersTest1 + +64: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +64: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +64: Test timeout computed to be: 1500 +test 65 + Start 65: testMolSupplier + +65: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +65: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +65: Test timeout computed to be: 1500 +59: [04:03:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +59: [04:03:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +59: [04:03:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +59: [04:03:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +59: [04:03:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +59: [04:03:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +59: [04:03:46] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [04:03:46] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +57: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +57: [04:03:46] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +57: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +59: [04:03:46] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +59: =============================================================================== +59: All tests passed (308 assertions in 9 test cases) +59: +57: [04:03:46] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +57: [04:03:46] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +65: [04:03:46] +65: ----------------------------------------- + 46/223 Test #59: nontetrahedralCatch .................... Passed 0.15 sec +test 66 + Start 66: testGeneralFileReader + +66: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +66: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +66: Test timeout computed to be: 1500 +27: ...[04:03:46] Molecule does not have explicit Hs. Consider calling AddHs() + 47/223 Test #57: smaTest1 ............................... Passed 0.20 sec +test 67 + Start 67: testMultithreadedMolSupplier + +67: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier +67: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +67: Test timeout computed to be: 1500 +27: [04:03:46] +27: +27: **** +27: Invariant Violation +27: bad direction in linearSearch +27: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h +27: Failed Expression: status >= 0 +27: **** +27: +64: *************************************** +64: *************************************** +64: [04:03:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: [04:03:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +58: [04:03:46] w block attempts to set wedging on bond 0 more than once. +58: [04:03:46] improperly formatted w block +65: [04:03:46] +65: +65: **** +65: Invariant Violation +65: bad prop value +65: Violation occurred on line 158 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +65: Failed Expression: nSwaps < 2 +65: **** +65: +67: [04:03:46] +67: ----------------------------------------- +58: [04:03:46] atom 3 is not associated with bond 1 in w block +66: [04:03:46] +66: ----------------------------------------- +66: [04:03:46] Finished: testDetermineFormat() +66: [04:03:46] ----------------------------------------- +66: +66: [04:03:46] +66: ----------------------------------------- +64: [04:03:46] bond with order 0 found on line 7. This is not part of the MDL specification. +63: Using new chirality perception +63: Test +63: +63: NewChiralTest.sdf +63: +63: Test +63: +63: NewChiralTest.sdf +63: +63: Test +63: +63: NewChiralTestNoChiral.sdf +63: +63: Test +63: +63: NewChiralTestNoChiral.sdf +63: +63: Test +63: +63: NewChiralTestAllChiral.sdf +63: +63: Test +63: +63: NewChiralTestAllChiral.sdf +63: +63: Test +63: +63: ProblemShort.mol +63: +63: [04:03:46] For a MultipleSgroup expansion, the matching orphaned bond was not found +63: The multiple sgroup will be ignored +58: =============================================================================== +58: All tests passed (1516 assertions in 53 test cases) +58: + 48/223 Test #58: smiTestCatch ........................... Passed 0.33 sec +test 68 + Start 68: testMolWriter + +68: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter +68: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +68: Test timeout computed to be: 1500 +54: --C1CCC2(CC1)CCCCC2CCC1CCCC1 +66: [04:03:46] Finished: testSdf() +66: [04:03:46] ----------------------------------------- +66: +66: [04:03:46] +66: ----------------------------------------- +64: [04:03:46] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +64: [04:03:46] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +64: [04:03:46] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +66: [04:03:46] Finished: testSmi() +66: [04:03:46] ----------------------------------------- +66: +66: [04:03:46] +66: ----------------------------------------- +64: generating smiles +64: 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 +64: converting back +54: smi: ClC1CCCCC1 +54: smi: ClC1CCCCC1 +54: smi: ClC1CCCCC1Br +54: smi: c1ccccc1 +54: smi: c1ccncc1 +54: smi: c1cc[nH]c1 +54: smi: c1cc[nH]c1 +54: smi: c1cc[pH]c1 +54: CbC(aC)aC +54: CaC(bC)aC +54: CbC(bC)aC +54: O.C +61: Randomness seeded to: 3187139666 +61: =============================================================================== +61: All tests passed (571 assertions in 14 test cases) +61: +54: 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 +54: [04:03:46] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +54: [04:03:46] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +54: [04:03:46] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +54: [04:03:46] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +54: [04:03:46] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +54: [04:03:46] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' + 49/223 Test #61: depictorCatch .......................... Passed 0.37 sec +test 69 + Start 69: testTplParser + +69: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser +69: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +69: Test timeout computed to be: 1500 +64: check isomorphism +54: [04:03:46] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +54: [04:03:46] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +54: [04:03:46] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +54: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +54: [04:03:46] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +54: [04:03:46] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +54: [04:03:46] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +54: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +54: [04:03:46] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +54: [04:03:46] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +54: [04:03:46] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +54: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +54: C=c1s/c2n(c1=O)CCCCCCC\N=2 +65: [04:03:46] Finished: testMolSup() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +54: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 +54: [04:03:46] SMILES Parse Error: extra close parentheses while parsing: C) +54: [04:03:46] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' + 50/223 Test #54: smiTest1 ............................... Passed 0.50 sec +test 70 + Start 70: testMol2ToMol + +70: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol +70: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +70: Test timeout computed to be: 1500 +65: [04:03:46] Finished: testRandMolSup() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- + 51/223 Test #69: testTplParser .......................... Passed 0.10 sec +test 71 + Start 71: testSequence + +71: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence +71: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +71: Test timeout computed to be: 1500 +27: ......[04:03:46] Molecule does not have explicit Hs. Consider calling AddHs() +27: [04:03:46] +27: +27: **** +27: Invariant Violation +27: bad direction in linearSearch +27: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h +27: Failed Expression: status >= 0 +27: **** +27: +65: [04:03:46] Finished: testSmilesSup() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +65: [04:03:46] ------------------------------------------------------ +65: [04:03:46] SMILES Parse Error: syntax error while parsing: fail +65: [04:03:46] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +65: [04:03:46] ERROR: Smiles parse error on line 3 +65: [04:03:46] ERROR: Cannot create molecule from : 'fail' +65: [04:03:46] ------------------------------------------------------ +65: [04:03:46] ------------------------------------------------------ +65: [04:03:46] >>> This may result in an infinite loop. It should finish almost immediately: +65: [04:03:46] <<< done. +65: [04:03:46] Finished: testSmilesSupFromText() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +66: [04:03:46] Finished: testMae() +66: [04:03:46] ----------------------------------------- +66: +66: [04:03:46] +66: ----------------------------------------- +65: [04:03:46] Finished: testSmilesWriter() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +66: [04:03:46] Finished: testTdt() +66: [04:03:46] ----------------------------------------- +66: 71: Sequence: GREG 71: HELM: PEPTIDE1{G.R.E.G}$$$$ 71: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O @@ -14874,97 +15331,6 @@ 71: ATOM 32 CG GLN A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 33 CD GLN A 4 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 34 OE1 GLN A 4 0.000 0.000 0.000 1.00 0.00 O - 37/223 Test #72: testExtendedStereoParsing .............. Passed 0.04 sec -test 78 - Start 78: connectTheDotsTest - -78: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest -78: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -78: Test timeout computed to be: 1500 -test 79 - Start 79: testSubstructMatch - -79: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -79: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct -79: Test timeout computed to be: 1500 -35: smi match: *1CC1 *1CC1 -35: smi match: O=COC=O O=COC=O -35: smi match: N=C=O N=C=O -35: smi match: N=C=S N=C=S -35: smi match: O~O O~O -35: smi match: N~[SiH4] N~[SiH4] -35: smi match: *P *P -35: smi match: C=N=N C=N=N -35: smi match: *N#[NH+] *N#[NH+] -35: smi match: *S* *S* -35: smi match: ** ** -35: smi match: *CC* *CC* -35: smi match: *O[SiH3] *O[SiH3] -35: smi match: *OS(*)~O *OS(*)~O -35: smi match: N~N~O N~N~O -35: smi match: *N(~O)(~O)~O *N(~O)(~O)~O -35: smi match: *[N+](=C)[O-] *[N+](=C)[O-] -35: smi match: * * -35: smi match: *C(*)NCN(*)* *C(*)NCN(*)* -35: smi match: *OCC#N *OCC#N -35: smi match: **C=C **C=C -35: smi match: C=C[O-] C=C[O-] -35: smi match: C=CO C=CO -35: smi match: * * -35: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O -35: smi match: O=COn1ccnc1 O=COn1ccnc1 -35: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F -35: smi match: CC(C)(C)S CC(C)(C)S -35: 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 -35: smi match: [CH]=O [CH]=O -35: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C -35: smi match: SS SS -35: smi match: [SH] [SH] -35: smi match: *C* *C* -35: smi match: * * -35: smi match: C[nH3+] C[nH3+] -35: smi match: cC(=N)[NH2] cC(=N)[NH2] -35: smi match: O=CN[OH] O=CN[OH] -35: smi match: NN NN -35: smi match: * * -35: smi match: *OP(=O)O* *OP(=O)O* -35: smi match: * * -35: smi match: * * -35: smi match: * * -35: smi match: *N=C(*)* *N=C(*)* -35: smi match: *C(*)(*)C=O *C(*)(*)C=O -35: smi match: CSC=O CSC=O -35: smi match: * * -35: smi match: O=CCl O=CCl -35: smi match: *** *** -35: smi match: *C=O *C=O -35: smi match: C[OH] C[OH] -35: smi match: C[OH] C[OH] -35: smi match: C[OH] C[OH] -35: smi match: C[OH] C[OH] -35: smi match: C[CH]=O C[CH]=O -35: smi match: *=* *=* -35: smi match: *C *C -35: smi match: C#C C#C -35: smi match: *[CH]C=C *[CH]C=C - 38/223 Test #44: graphmolTestsCatch ..................... Passed 0.15 sec -33: [07:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors -33: ------------------------------- -33: [07:34:57] Explicit valence for atom # 0 N, 4, is greater than permitted -33: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -33: [07:34:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -33: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -33: [07:34:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -15: ......... -15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.014s -15: -15: OK -14: ......... -14: ---------------------------------------------------------------------- -14: Ran 9 tests in 0.008s -14: -14: OK 71: ATOM 35 NE2 GLN A 4 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 36 N ASN A 5 0.000 0.000 0.000 1.00 0.00 N 71: ATOM 37 CA ASN A 5 0.000 0.000 0.000 1.00 0.00 C @@ -15104,6 +15470,13 @@ 71: ATOM 48 CD1 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 49 CD2 LEU A 6 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 50 N DPN A 7 0.000 0.000 0.000 1.00 0.00 N + 52/223 Test #66: testGeneralFileReader .................. Passed 0.41 sec +test 72 + Start 72: testExtendedStereoParsing + +72: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing +72: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +72: Test timeout computed to be: 1500 71: HETATM 51 CA DPN A 7 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 52 C DPN A 7 0.000 0.000 0.000 1.00 0.00 C 71: HETATM 53 O DPN A 7 0.000 0.000 0.000 1.00 0.00 O @@ -15251,1616 +15624,128 @@ 71: CONECT 27 28 28 29 71: END 71: -64: [07:34:57] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -64: [07:34:57] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -64: [07:34:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -64: generating smiles -64: 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 -64: converting back -64: check isomorphism -74: Randomness seeded to: 3484029761 -74: =============================================================================== -74: All tests passed (95 assertions in 4 test cases) -74: -63: Using new chirality perception -63: Test -63: -63: NewChiralTest.sdf -63: -63: Test -63: -63: NewChiralTest.sdf -63: -63: Test -63: -63: NewChiralTestNoChiral.sdf -63: -63: Test -63: -63: NewChiralTestNoChiral.sdf -63: -63: Test -63: -63: NewChiralTestAllChiral.sdf -63: -63: Test -63: -63: NewChiralTestAllChiral.sdf -63: -63: Test -63: -63: ProblemShort.mol -63: -63: [07:34:57] For a MultipleSgroup expansion, the matching orphaned bond was not found -63: The multiple sgroup will be ignored -23: ..... -23: ---------------------------------------------------------------------- -23: Ran 5 tests in 0.002s -23: -23: OK -23: Testing Alignment Wrapper code: -73: Randomness seeded to: 781856005 -73: [07:34:57] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -73: [07:34:57] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -73: [07:34:57] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -73: [07:34:57] SGroup 1 is invalid and will be ignored -73: [07:34:57] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -73: [07:34:57] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -73: [07:34:57] SGroup 1 is invalid and will be ignored -73: [07:34:57] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -73: [07:34:57] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -73: [07:34:57] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -73: [07:34:57] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -73: [07:34:57] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -73: [07:34:57] SGroup 1 is invalid and will be ignored -73: [07:34:57] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -73: [07:34:57] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -73: [07:34:57] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -73: [07:34:57] SGroup 1 is invalid and will be ignored -73: [07:34:57] SGroup 3 referenced on line 40 not found. -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: no bonds -73: Violation occurred on line 139 in file ./Code/GraphMol/SubstanceGroup.cpp -73: Failed Expression: !d_bonds.empty() -73: **** -73: -73: [07:34:57] SGroup 3 referenced on line 40 not found. -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: no bonds -73: Violation occurred on line 139 in file ./Code/GraphMol/SubstanceGroup.cpp -73: Failed Expression: !d_bonds.empty() -73: **** -73: -73: [07:34:57] no bonds -73: [07:34:57] SGroup 1 is invalid and will be ignored -73: [07:34:57] SGroup line too short: 'M SBV 1 6' on line 42 -73: [07:34:57] SGroup 1 is invalid and will be ignored -73: [07:34:57] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -73: [07:34:57] SGroup 2 is invalid and will be ignored -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: bookmark not found -73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp -73: Failed Expression: (lu != d_bondBookmarks.end()) -73: **** -73: -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: bookmark not found -73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp -73: Failed Expression: (lu != d_bondBookmarks.end()) -73: **** -73: -73: [07:34:57] bookmark not found -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: bond is not part of the SubstanceGroup -73: Violation occurred on line 158 in file ./Code/GraphMol/SubstanceGroup.cpp -73: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() -73: **** -73: -73: [07:34:57] bond is not part of the SubstanceGroup -73: [07:34:57] SGroup 2 is invalid and will be ignored -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: bookmark not found -73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp -73: Failed Expression: (lu != d_atomBookmarks.end()) -73: **** -73: -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: bookmark not found -73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp -73: Failed Expression: (lu != d_atomBookmarks.end()) -73: **** -73: -73: [07:34:57] bookmark not found -73: [07:34:57] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -73: [07:34:57] SGroup 2 is invalid and will be ignored -73: [07:34:57] WARNING: final character of V3000 array is not ')' -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: bookmark not found -73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp -73: Failed Expression: (lu != d_bondBookmarks.end()) -73: **** -73: -73: [07:34:57] WARNING: final character of V3000 array is not ')' -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: bookmark not found -73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp -73: Failed Expression: (lu != d_bondBookmarks.end()) -73: **** -73: -73: [07:34:57] bookmark not found -73: [07:34:57] SGroup 1 is invalid and will be ignored -73: [07:34:57] WARNING: final character of V3000 array is not ')' -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: bookmark not found -73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp -73: Failed Expression: (lu != d_atomBookmarks.end()) -73: **** -73: -73: [07:34:57] WARNING: final character of V3000 array is not ')' -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: bookmark not found -73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp -73: Failed Expression: (lu != d_atomBookmarks.end()) -73: **** -73: -73: [07:34:57] bookmark not found -73: [07:34:57] SGroup 1 is invalid and will be ignored -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: bookmark not found -73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp -73: Failed Expression: (lu != d_bondBookmarks.end()) -73: **** -73: -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: bookmark not found -73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp -73: Failed Expression: (lu != d_bondBookmarks.end()) -73: **** -73: -73: [07:34:57] bookmark not found -73: [07:34:57] SGroup 2 is invalid and will be ignored -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: bookmark not found -73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp -73: Failed Expression: (lu != d_atomBookmarks.end()) -73: **** -73: -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: bookmark not found -73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp -73: Failed Expression: (lu != d_atomBookmarks.end()) -73: **** -73: -73: [07:34:57] bookmark not found -73: [07:34:57] SGroup 2 is invalid and will be ignored -73: [07:34:57] Explicit valence for atom # 2 O, 3, is greater than permitted -73: [07:34:57] Explicit valence for atom # 1 O, 3, is greater than permitted -73: [07:34:57] Explicit valence for atom # 1 C, 5, is greater than permitted -73: [07:34:57] sanitize [07:34:57] UNK: [07:34:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -3: .... -3: ---------------------------------------------------------------------- -3: Ran 4 tests in 0.029s -3: -3: OK -13: ...... -13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.002s -13: -13: OK - 39/223 Test #70: testMol2ToMol .......................... Passed 0.09 sec - 40/223 Test #71: testSequence ........................... Passed 0.08 sec - 41/223 Test #74: testPropertyLists ...................... Passed 0.07 sec -test 80 - Start 80: substructTestCatch - -80: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch -80: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct -80: Test timeout computed to be: 1500 -test 81 - Start 81: testGenericGroups - -81: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups -81: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups -81: Test timeout computed to be: 1500 -test 82 - Start 82: testReaction - -82: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction -82: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -82: Test timeout computed to be: 1500 -test 83 - Start 83: testReactionFingerprints - -83: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints -83: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -83: Test timeout computed to be: 1500 -35: smi match: cCC(=O)[OH] cCC(=O)[OH] -35: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] -35: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] -35: smi match: C=CC(=O)[OH] C=CC(=O)[OH] -35: smi match: N#CC(=O)[OH] N#CC(=O)[OH] -35: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O -35: smi match: *N(*)C*=O *N(*)C*=O -35: smi match: O=*C[OH] O=*C[OH] -35: smi match: *=C*=O *=C*=O -35: smi match: *=CC#N *=CC#N -35: smi match: *C[OH] *C[OH] -35: smi match: ** ** -35: smi match: *C[OH] *C[OH] -35: smi match: *C(*)=O *C(*)=O -35: smi match: * * -35: smi match: *CC(=O)[OH] *CC(=O)[OH] -35: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O -35: smi match: *c *c -35: smi match: CN(C)c CN(C)c -35: smi match: c c -35: smi match: *c *c -35: smi match: *c *c -35: smi match: **:*cF **:*cF -35: smi match: cB([OH])[OH] cB([OH])[OH] -35: smi match: N~N~N N~N~N -35: smi match: *N=N* *N=N* -35: smi match: *CC[OH] *CC[OH] -35: smi match: *CC[OH] *CC[OH] -35: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] -35: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] -35: smi match: *CCC(=O)[OH] *CCC(=O)[OH] -35: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] -35: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O -35: smi match: *OC(*)=O *OC(*)=O -35: smi match: *C(=O)[OH] *C(=O)[OH] -35: smi match: O=C[OH] O=C[OH] -35: smi match: *OC(=O)O* *OC(=O)O* -35: smi match: * * -35: smi match: *OC(=O)Cl *OC(=O)Cl -35: smi match: *C#N *C#N -35: smi match: NCC(=O)NCC=O NCC(=O)NCC=O -35: smi match: SS SS -35: smi match: * * -35: smi match: *=* *=* -35: smi match: *=* *=* -35: smi match: *=* *=* -35: smi match: *=* *=* -35: smi match: C1CO1 C1CO1 -35: smi match: *OC(*)=O *OC(*)=O -35: smi match: * * -35: smi match: *O*[OH] *O*[OH] -35: smi match: COC(C)(C)O COC(C)(C)O -35: smi match: *[OH] *[OH] -35: smi match: ** ** -35: smi match: C=N[NH2] C=N[NH2] -35: smi match: C=NC=O C=NC=O -35: smi match: * * -35: smi match: C#NC C#NC -35: smi match: CN=C=O CN=C=O -35: smi match: CN=C=S CN=C=S -35: smi match: *OC(*)(*)O* *OC(*)(*)O* -35: smi match: *C(*)=O *C(*)=O -35: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C -35: smi match: *~*=O *~*=O -35: smi match: *~*=O *~*=O -35: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] -35: smi match: * * -35: smi match: *C#N *C#N -35: smi match: *N(=O)~O *N(=O)~O -35: smi match: N N -35: smi match: OC(=O)C(O)=O OC(=O)C(O)=O -35: smi match: C=NO C=NO -35: smi match: O~O O~O -35: smi match: c[OH] c[OH] -35: smi match: O=P(~[OH])~O O=P(~[OH])~O -35: smi match: CO~P(=O)~O CO~P(=O)~O -35: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O -35: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O -35: smi match: O=P(~O)~O O=P(~O)~O -35: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O -35: smi match: C[NH2] C[NH2] -35: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 -35: smi match: * * -35: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 -35: smi match: CS(C)~O CS(C)~O -35: smi match: CS(C)(~O)~O CS(C)(~O)~O -35: smi match: CS(N)(~O)~O CS(N)(~O)~O -35: smi match: CS([OH])(~O)~O CS([OH])(~O)~O -35: smi match: COS(C)(~O)~O COS(C)(~O)~O -35: smi match: *S(C)(~O)~O *S(C)(~O)~O -35: smi match: CN(C)C CN(C)C -35: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 -35: smi match: *C(*)=S *C(*)=S -35: smi match: *OC(*)=S *OC(*)=S -33: [07:34:57] WARNING: not removing hydrogen atom with dummy atom neighbors -73: [07:34:57] skipping block at line 7: 'BEGIN ATOM' -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: no stream -73: Violation occurred on line 144 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp -73: Failed Expression: dp_inStream -73: **** -73: -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: no stream -73: Violation occurred on line 179 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp -73: Failed Expression: dp_inStream -73: **** -73: -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: no stream -73: Violation occurred on line 427 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp -73: Failed Expression: dp_inStream -73: **** -73: -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: no stream -73: Violation occurred on line 274 in file ./Code/GraphMol/FileParsers/TDTMolSupplier.cpp -73: Failed Expression: dp_inStream -73: **** -73: -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: no stream -73: Violation occurred on line 515 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -73: Failed Expression: dp_sInStream != nullptr -73: **** -73: -73: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 21 -73: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 20 -73: [07:34:57] -73: -73: **** -73: Post-condition Violation -73: Element '' not found -73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -73: Failed Expression: anum > -1 -73: **** -73: -73: [07:34:57] BEGIN SGROUP line not found on line 14 -73: [07:34:57] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -73: [07:34:57] END SGROUP line not found on line 14 -73: [07:34:57] END SGROUP line not found on line 14 -73: [07:34:57] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -73: [07:34:57] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -73: [07:34:57] -73: -73: **** -73: Range Error -73: idx -73: Violation occurred on line 328 in file ./Code/GraphMol/ROMol.cpp -73: Failed Expression: 99 < 9 -73: **** -73: -73: [07:34:57] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -73: [07:34:57] Multiple ATTCHPT values for atom 2 on line 9 -73: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 12 -73: [07:34:57] SMARTS Parse Error: syntax error while parsing: [#6;R -73: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -73: [07:34:57] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -73: [07:34:57] Skipping empty SMARTS value for SMARTSQ. -73: [07:34:57] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -73: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 12 -75: Randomness seeded to: 2209681215 -75: =============================================================================== -75: All tests passed (100 assertions in 2 test cases) -75: - 42/223 Test #75: XYZFileParserCatchTest ................. Passed 0.07 sec -58: [07:34:57] w block attempts to set wedging on bond 0 more than once. -58: [07:34:57] improperly formatted w block -58: [07:34:57] atom 3 is not associated with bond 1 in w block -58: =============================================================================== -58: All tests passed (1516 assertions in 53 test cases) -58: -25: done - 43/223 Test #25: testUFFForceField ...................... Passed 0.25 sec -77: Randomness seeded to: 2285883672 -77: [07:34:57] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -77: [07:34:57] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -77: [07:34:57] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -77: [07:34:57] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -77: [07:34:57] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 2 ignored -77: =============================================================================== -77: All tests passed (142 assertions in 6 test cases) -77: - 44/223 Test #77: molfileStereoCatchTest ................. Passed 0.06 sec -29: ...... -29: ---------------------------------------------------------------------- -29: Ran 6 tests in 0.001s -29: -29: OK -57: [07:34:57] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -57: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -57: [07:34:57] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -57: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -57: [07:34:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -57: [07:34:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -78: Randomness seeded to: 3254685953 -78: =============================================================================== -78: All tests passed (8 assertions in 1 test case) -78: - 45/223 Test #78: connectTheDotsTest ..................... Passed 0.05 sec -79: ----------------- Test 1 -79: Done -79: -79: ----------------- Test 2 -79: Done -79: -79: ----------------- Test 3 -79: Done -79: -79: ----------------- Test 4 -79: Done -79: -79: ----------------- Test 5 -79: Done -79: -79: ----------------- Test 5 QueryRoot -79: Done -79: -79: ----------------- Test 6 (Issue71 related) -79: Done -79: -79: ----------------- Testing serial numbers on recursive queries -79: Done -79: -79: [07:34:57] ------------------------------------- -79: [07:34:57] Test multithreading -79: reading molecules -66: [07:34:57] Finished: testMae() -66: [07:34:57] ----------------------------------------- -66: -66: [07:34:57] -66: ----------------------------------------- -66: [07:34:57] Finished: testTdt() -66: [07:34:57] ----------------------------------------- -66: -54: --C1CCC2(CC1)CCCCC2CCC1CCCC1 - 46/223 Test #14: pySparseIntVect ........................ Passed 0.27 sec - 47/223 Test #15: pyFPB .................................. Passed 0.27 sec - 48/223 Test #57: smaTest1 ............................... Passed 0.16 sec -test 84 - Start 84: testEnumeration - -84: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration -84: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -84: Test timeout computed to be: 1500 -test 85 - Start 85: rxnTestCatch - -85: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch -85: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -85: Test timeout computed to be: 1500 -test 86 - Start 86: pyChemReactions - -86: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" -86: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -86: Test timeout computed to be: 1500 -test 87 - Start 87: pyChemReactionEnumerations - -87: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" -87: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -87: Test timeout computed to be: 1500 -test 88 - Start 88: pyChemReactionSanitize - -88: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" -88: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -88: Test timeout computed to be: 1500 -test 89 - Start 89: testChemTransforms - -89: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms -89: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms -89: Test timeout computed to be: 1500 -test 90 - Start 90: chemTransformsTestCatch - -90: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -90: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms -90: Test timeout computed to be: 1500 -35: smi match: * * -35: smi match: C[SH] C[SH] -35: smi match: c[SH] c[SH] -35: smi match: NC(N)=S NC(N)=S -35: smi match: * * -35: smi match: ***** ***** -35: smi match: NC(N)=O NC(N)=O -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing sf.net issue 280. -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing sf.net issue 285. -35: [07:34:57] done -35: [07:34:57] done -35: [07:34:57] done -35: [07:34:57] done -35: [07:34:57] done -35: [07:34:57] done -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing Github2441: Add RDProps interface to Conformers. -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing Issue2510: Pickle Confs as double. -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing loading pickled mols with conformers -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing conformer reading/writing options -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing property reading options -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing property reading options -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing boost::serialization integration -35: [07:34:57] done -35: [07:34:57] ------------------------------------- -35: [07:34:57] Testing github issue 6036 -73: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -73: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: [07:34:57] WARNING: Skipping property bar because the value includes an illegal blank line -73: [07:34:57] WARNING: Skipping property baz because the value includes an illegal blank line -73: [07:34:57] WARNING: Skipping property bletch -73: nope because the name includes a newline -73: [07:34:57] WARNING: Skipping property bletch -73: nope2 because the name includes a newline -73: [07:34:57] -73: -73: **** -73: Post-condition Violation -73: Element 'QQQ' not found -73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -73: Failed Expression: anum > -1 -73: **** -73: -73: [07:34:57] -73: -73: **** -73: Post-condition Violation -73: Element 'QQQ' not found -73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -73: Failed Expression: anum > -1 -73: **** -73: -73: [07:34:57] -73: -73: **** -73: Post-condition Violation -73: Element 'QQQ' not found -73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -73: Failed Expression: anum > -1 -73: **** -73: -73: [07:34:57] -73: -73: **** -73: Post-condition Violation -73: Element 'QQQ' not found -73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -73: Failed Expression: anum > -1 -73: **** -73: -73: [07:34:57] atom 3 has a negative isotope value. line: 15 -73: [07:34:57] -73: -73: **** -73: Invariant Violation -73: bad prop value -73: Violation occurred on line 158 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -73: Failed Expression: nSwaps < 2 -73: **** -73: -73: [07:34:57] -73: -73: **** -73: Pre-condition Violation -73: no input stream -73: Violation occurred on line 480 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -73: Failed Expression: dp_sInStream -73: **** -73: - 49/223 Test #58: smiTestCatch ........................... Passed 0.18 sec -19: ........... -19: ---------------------------------------------------------------------- -19: Ran 11 tests in 0.026s -19: -19: OK -19: Testing Geometry wrapper - 50/223 Test #66: testGeneralFileReader .................. Passed 0.15 sec -54: smi: ClC1CCCCC1 -54: smi: ClC1CCCCC1 -54: smi: ClC1CCCCC1Br -54: smi: c1ccccc1 -54: smi: c1ccncc1 -54: smi: c1cc[nH]c1 -54: smi: c1cc[nH]c1 -54: smi: c1cc[pH]c1 -76: Randomness seeded to: 2719823162 -76: [07:34:57] Invalid or missing fragment id from CDXML fragment, assigning new one... -76: [07:34:57] Explicit valence for atom # 3 N, 4, is greater than permitted -76: [07:34:57] CDXMLParser: failed sanitizing skipping fragment 32 -76: [07:34:57] Bad bond in CDXML skipping fragment 58... -76: [07:34:57] Invalid or missing fragment id from CDXML fragment, assigning new one... -76: [07:34:57] Bad bond in CDXML skipping fragment 58... -61: Randomness seeded to: 2713940792 -61: =============================================================================== -61: All tests passed (571 assertions in 14 test cases) -61: -65: [07:34:57] Finished: testMolSup() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testRandMolSup() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -83: [07:34:57] ------------------------------------- -83: [07:34:57] Test Reaction StructuralFingerprint - 51/223 Test #13: pyDiscreteValueVect .................... Passed 0.29 sec - 52/223 Test #23: pyAlignment ............................ Passed 0.28 sec - 53/223 Test #35: graphmoltestPickler .................... Passed 0.25 sec - 54/223 Test #61: depictorCatch .......................... Passed 0.16 sec -test 91 - Start 91: tautomerQueryTestCatch - -91: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch -91: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery -91: Test timeout computed to be: 1500 -test 92 - Start 92: pyTautomerQuery - -92: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" -92: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap -92: Test timeout computed to be: 1500 -test 93 - Start 93: testSubgraphs1 - -93: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 -93: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -93: Test timeout computed to be: 1500 -test 94 - Start 94: testSubgraphs2 - -94: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 -94: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -94: Test timeout computed to be: 1500 -test 95 - Start 95: subgraphsCatch - -95: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch -95: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -95: Test timeout computed to be: 1500 -test 96 - Start 96: filterCatalogTest - -96: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest -96: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog -96: Test timeout computed to be: 1500 -54: CbC(aC)aC -54: CaC(bC)aC -54: CbC(bC)aC -54: O.C -54: 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 -54: [07:34:57] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -54: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -54: [07:34:57] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -54: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -54: [07:34:57] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -54: [07:34:57] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -54: [07:34:57] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -54: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -54: [07:34:57] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -54: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -54: [07:34:57] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -54: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -54: [07:34:57] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -54: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -54: [07:34:57] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -54: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -54: [07:34:57] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -54: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -54: C=c1s/c2n(c1=O)CCCCCCC\N=2 -54: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -54: [07:34:57] SMILES Parse Error: extra close parentheses while parsing: C) -54: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' -76: [07:34:57] WARNING: not removing hydrogen atom without neighbors -76: [07:34:57] WARNING: not removing hydrogen atom without neighbors -76: [07:34:57] WARNING: not removing hydrogen atom without neighbors -76: [07:34:57] WARNING: not removing hydrogen atom without neighbors -76: [07:34:57] WARNING: not removing hydrogen atom without neighbors -76: [07:34:57] WARNING: not removing hydrogen atom without neighbors -76: [07:34:57] WARNING: not removing hydrogen atom without neighbors -76: [07:34:57] WARNING: not removing hydrogen atom without neighbors -76: [07:34:57] WARNING: not removing hydrogen atom without neighbors -76: [07:34:57] WARNING: not removing hydrogen atom without neighbors -83: [07:34:57] ------------------------------------- -83: [07:34:57] Test Reaction DifferenceFingerprint - 55/223 Test #3: pyCoordGen ............................. Passed 0.33 sec -79: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -79: processing -79: launch :0 -79: launch :1 -79: launch :2 -79: launch :3 -82: smi: O=C1CNC(=O)CN1 -82: 1: O=C1CNC(=O)CN1 -82: 2: COOC -82: [07:34:57] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -82: [07:34:57] 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]' -82: O=C1CNC(=O)CN1 -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] mapped atoms in the reactants were not mapped in the products. -82: unmapped numbers are: 4 -82: [07:34:57] atom 0 in product 0 has multiple charge specifications. -82: mass: 15.0001 -82: Oc1ccccn1 -82: Oc1ccc[nH]1 -93: ----------------------- -93: Subgraph retrieval -93: Finished -93: ----------------------- -93: testSubgraphs2a - 56/223 Test #29: pyDistGeom ............................. Passed 0.29 sec - 57/223 Test #54: smiTest1 ............................... Passed 0.21 sec - 58/223 Test #83: testReactionFingerprints ............... Passed 0.05 sec -test 97 - Start 97: pyFilterCatalog - -97: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" -97: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap -97: Test timeout computed to be: 1500 -test 98 - Start 98: testFragCatalog - -98: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -98: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog -98: Test timeout computed to be: 1500 -test 99 - Start 99: pyFragCatalog - -99: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/rough_test.py" -99: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap -99: Test timeout computed to be: 1500 -test 100 - Start 100: testDescriptors - -100: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors -100: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -100: Test timeout computed to be: 1500 -76: [07:34:57] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. -76: [07:34:57] Incomplete atom labelling, cannot make bond -76: [07:34:57] Incomplete atom labelling, cannot make bond -82: [07:34:57] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -82: [07:34:57] SMARTS Parse Error: syntax error while parsing: ([C:2] -82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -82: [07:34:57] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -82: [07:34:57] SMARTS Parse Error: syntax error while parsing: [C:2]) -82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -82: [07:34:57] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -82: [07:34:57] 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]' -82: [07:34:57] reactant 2 has no mapped atoms. -82: [07:34:57] >> Atoms within one molecule have different RXN roles. -82: [07:34:57] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -82: [07:34:57] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -82: [07:34:57] SMARTS Parse Error: syntax error while parsing: ([C:2] -82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -82: [07:34:57] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -82: [07:34:57] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -82: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -93: Finished -93: ----------------------- -93: testSubgraphs2 -94: ----------------------- -94: Test1: pathToSubmol -94: Finished -94: ----------------------- -94: Test2: Atom Environments -94: Finished -94: ----------------------- -94: Test 3: Atom Environments (Extension) -94: Finished -94: ----------------------- -94: Testing github Issue103: stereochemistry and pathToSubmol -94: Finished -94: ----------------------- -94: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) -94: Finished -89: 1 smi: CC -89: 1 smi: CC -89: 2 smi: CCO[C@H](N)P -89: 2 smi: CC -89: replaceSub smi1:CCP(CC)[C@@H](N)O -89: replaceSub smi1:CCNCC -89: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O -89: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O -89: [07:34:57] SMARTS Parse Error: syntax error while parsing: bar -89: [07:34:57] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -65: [07:34:57] Finished: testSmilesSup() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] ------------------------------------------------------ -65: [07:34:57] SMILES Parse Error: syntax error while parsing: fail -65: [07:34:57] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -65: [07:34:57] ERROR: Smiles parse error on line 3 -65: [07:34:57] ERROR: Cannot create molecule from : 'fail' -65: [07:34:57] ------------------------------------------------------ -65: [07:34:57] ------------------------------------------------------ -65: [07:34:57] >>> This may result in an infinite loop. It should finish almost immediately: -65: [07:34:57] <<< done. -65: [07:34:57] Finished: testSmilesSupFromText() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testSmilesWriter() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -95: Randomness seeded to: 2870800801 -95: --------- -95: =============================================================================== -95: All tests passed (11 assertions in 1 test case) -95: -85: Randomness seeded to: 3603752063 -85: [07:34:57] atom 0 in product 0 has multiple charge specifications. -85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 34 -85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 36 -85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 38 -85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 40 -85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 42 -85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 87 -85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 89 -85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 91 -85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 93 -85: [07:34:57] Found a SCD/SED line with missing/empty SDT specification at line 95 -90: Randomness seeded to: 1287606086 -90: [07:34:57] Incomplete atom labelling, cannot make bond -90: [07:34:57] -90: -90: **** -90: Invariant Violation -90: molzip: bond info already exists for end atom with label:1 -90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -90: Failed Expression: !bond.b -90: **** -90: - 59/223 Test #94: testSubgraphs2 ......................... Passed 0.03 sec - 60/223 Test #95: subgraphsCatch ......................... Passed 0.03 sec -test 101 - Start 101: testAUTOCORR2D - -101: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D -101: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -101: Test timeout computed to be: 1500 -test 102 - Start 102: testATF - -102: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF -102: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -102: Test timeout computed to be: 1500 -82: [07:34:57] reactant 0 has no mapped atoms. -82: [07:34:57] reactant 1 has no mapped atoms. -82: [07:34:57] reactant 3 has no mapped atoms. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 4 found multiple times. -82: [07:34:57] product atom-mapping number 5 found multiple times. -82: [07:34:57] product atom-mapping number 6 found multiple times. -82: [07:34:57] product atom-mapping number 7 found multiple times. -82: [07:34:57] product atom-mapping number 8 found multiple times. -82: [07:34:57] product atom-mapping number 12 found multiple times. -82: [07:34:57] product atom-mapping number 9 found multiple times. -82: [07:34:57] product atom-mapping number 10 found multiple times. -82: [07:34:57] product atom-mapping number 11 found multiple times. -82: [07:34:57] reactant 0 has no mapped atoms. -82: [07:34:57] reactant 1 has no mapped atoms. -82: [07:34:57] reactant 3 has no mapped atoms. -82: [07:34:57] reactant atom-mapping number 19 found multiple times. -82: [07:34:57] reactant atom-mapping number 25 found multiple times. -82: [07:34:57] reactant atom-mapping number 20 found multiple times. -82: [07:34:57] reactant atom-mapping number 21 found multiple times. -82: [07:34:57] reactant atom-mapping number 22 found multiple times. -82: [07:34:57] reactant atom-mapping number 23 found multiple times. -82: [07:34:57] reactant atom-mapping number 24 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -82: [07:34:57] product atom-mapping number 5 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 4 found multiple times. -82: [07:34:57] product atom-mapping number 5 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 4 found multiple times. -82: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -82: [07:34:57] product atom-mapping number 5 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 4 found multiple times. -82: [07:34:57] product atom-mapping number 5 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 4 found multiple times. -82: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 4 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 4 found multiple times. -82: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 4 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 4 found multiple times. -82: F[C@](Cl)(Br)O[C@](F)(Cl)Br -82: [07:34:57] product atom-mapping number 4 found multiple times. -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 4 found multiple times. -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 4 found multiple times. -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 4 found multiple times. -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] mapped atoms in the reactants were not mapped in the products. -82: unmapped numbers are: 4 -82: [07:34:57] product atom-mapping number 3 found multiple times. -82: [07:34:57] product atom-mapping number 2 found multiple times. -82: [07:34:57] product atom-mapping number 1 found multiple times. -82: [07:34:57] mapped atoms in the reactants were not mapped in the products. -82: unmapped numbers are: 4 -82: [07:34:57] product atom-mapping number 6 not found in reactants. -82: [07:34:57] product atom-mapping number 7 not found in reactants. -82: [07:34:57] product atom-mapping number 8 not found in reactants. -82: [07:34:57] product atom-mapping number 7 not found in reactants. -82: [07:34:57] product atom-mapping number 8 not found in reactants. -82: [07:34:57] product atom-mapping number 9 not found in reactants. -82: [07:34:57] product atom-mapping number 10 not found in reactants. -82: [07:34:57] mapped atoms in the reactants were not mapped in the products. -82: unmapped numbers are: 6 -82: [07:34:57] product atom-mapping number 7 not found in reactants. -82: [07:34:57] product atom-mapping number 8 not found in reactants. -82: [07:34:57] product atom-mapping number 9 not found in reactants. -82: [07:34:57] product atom-mapping number 10 not found in reactants. -82: [07:34:57] mapped atoms in the reactants were not mapped in the products. -82: unmapped numbers are: 6 -65: [07:34:57] Finished: testSDWriter() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testSDSupplierEnding() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testSuppliersEmptyFile() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testCisTrans() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testStereoRound() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -65: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -65: [07:34:57] Finished: testIssue226() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -85: [07:34:57] mapped atoms in the reactants were not mapped in the products. -85: unmapped numbers are: 2 -85: [07:34:57] mapped atoms in the reactants were not mapped in the products. -85: unmapped numbers are: 2 -85: [07:34:57] SMARTS Parse Error: unclosed ring for input: 'CC1' -85: [07:34:57] SMILES Parse Error: unclosed ring for input: 'CC1' -85: [07:34:57] mapped atoms in the reactants were not mapped in the products. -85: unmapped numbers are: 2 -85: [07:34:57] product atom-mapping number 2 not found in reactants. -85: [07:34:57] mapped atoms in the reactants were not mapped in the products. -85: unmapped numbers are: 2 -85: [07:34:57] product atom-mapping number 2 not found in reactants. -90: [07:34:57] Incomplete atom labelling, cannot make bond -90: [07:34:57] -90: -90: **** -90: Invariant Violation -90: molzip: bond info already exists for end atom with label:1 -90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -90: Failed Expression: !bond.b -90: **** -90: - 61/223 Test #19: testPyGeometry ......................... Passed 0.34 sec -test 103 - Start 103: testBCUT - -103: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT -103: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -103: Test timeout computed to be: 1500 -82: 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] -82: 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] -65: [07:34:57] Finished: testTDTSupplier1() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testTDTSupplier2() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testTDTSupplier3() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testSDSupplierFromText() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] ERROR: Problems encountered parsing data fields -65: [07:34:57] ERROR: moving to the beginning of the next molecule -65: [07:34:57] ERROR: Problems encountered parsing data fields -65: [07:34:57] ERROR: moving to the beginning of the next molecule -65: [07:34:57] Spurious data before the first property will be ignored -65: [07:34:57] Property will be truncated after the first blank line -65: [07:34:57] Property will be truncated after the first blank line -65: [07:34:57] Property will be truncated after the first blank line -65: [07:34:57] Finished: testSDSupplierStrLax1() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] ERROR: Problems encountered parsing data fields -65: [07:34:57] ERROR: moving to the beginning of the next molecule -65: [07:34:57] Property will be truncated after the first blank line -65: [07:34:57] Finished: testSDSupplierStrLax2() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] ERROR: Problems encountered parsing data fields -65: [07:34:57] ERROR: moving to the beginning of the next molecule -65: [07:34:57] ERROR: Problems encountered parsing data fields -65: [07:34:57] ERROR: moving to the beginning of the next molecule -65: [07:34:57] Spurious data before the first property will be ignored -65: [07:34:57] Property will be truncated after the first blank line -65: [07:34:57] Property will be truncated after the first blank line -65: [07:34:57] Property will be truncated after the first blank line -65: [07:34:57] Finished: testSDSupplierFromTextStrLax1() -65: [07:34:57] ----------------------------------------- +65: [04:03:46] Finished: testSDWriter() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] ERROR: Problems encountered parsing data fields -65: [07:34:57] ERROR: moving to the beginning of the next molecule -65: [07:34:57] Property will be truncated after the first blank line -65: [07:34:57] Finished: testSDSupplierFromTextStrLax2() -65: [07:34:57] ----------------------------------------- +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testSDSupplierEnding() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testIssue265() -65: [07:34:57] ----------------------------------------- +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testSuppliersEmptyFile() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] ERROR: End of data field name not found -65: [07:34:57] ERROR: moving to the beginning of the next molecule -85: [07:34:57] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -73: [07:34:57] ERROR: molecules without atoms cannot be exported to Maestro files. -73: [07:34:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -73: [07:34:57] ERROR: the mol cannot be kekulized, and will not be written to the output file. -73: [07:34:57] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. -73: [07:34:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -73: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: [07:34:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -100: [07:34:57] ------------------------------------- -100: [07:34:57] Test Crippen parameter acquisition. -65: [07:34:57] Explicit valence for atom # 0 F, 2, is greater than permitted -65: [07:34:57] ERROR: Could not sanitize molecule ending on line 16 -65: [07:34:57] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -73: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -65: [07:34:57] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -65: [07:34:57] ERROR: moving to the beginning of the next molecule -65: [07:34:57] ERROR: Bond line too short: 'M END' on line 18 -65: [07:34:57] ERROR: moving to the beginning of the next molecule -65: [07:34:57] Finished: testSDErrorHandling() -65: [07:34:57] ----------------------------------------- +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testCisTrans() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -73: =============================================================================== -73: All tests passed (1311 assertions in 87 test cases) -73: -76: [07:34:57] Incomplete atom labelling, cannot make bond -100: [07:34:57] done -100: [07:34:57] ------------------------------------- -100: [07:34:57] Test Crippen calculation. -85: =============================================================================== -85: All tests passed (568 assertions in 20 test cases) -85: -98: 21 - 62/223 Test #73: fileParsersCatchTest ................... Passed 0.18 sec - 63/223 Test #85: rxnTestCatch ........................... Passed 0.09 sec -test 104 - Start 104: testEEM - -104: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM -104: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -104: Test timeout computed to be: 1500 -test 105 - Start 105: testPBF +65: [04:03:46] ----------------------------------------- +4: dynamic RDAny:0.463389 s +4: static RDValue:2e-06 s + 53/223 Test #71: testSequence ........................... Passed 0.08 sec +test 73 + Start 73: fileParsersCatchTest -105: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF -105: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -105: Test timeout computed to be: 1500 -65: [07:34:57] Finished: testIssue381() -65: [07:34:57] ----------------------------------------- +73: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +73: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +73: Test timeout computed to be: 1500 + 54/223 Test #70: testMol2ToMol .......................... Passed 0.17 sec +65: [04:03:46] Finished: testStereoRound() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testSetStreamIndices() -65: [07:34:57] ----------------------------------------- +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +65: [04:03:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +65: [04:03:46] Finished: testIssue226() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testMixIterAndRandom() -65: [07:34:57] ----------------------------------------- +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testTDTSupplier1() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -65: build: -65: [07:34:57] Finished: testRemoveHs() -65: [07:34:57] ----------------------------------------- +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testTDTSupplier2() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -90: [07:34:57] Incomplete atom labelling, cannot make bond -90: [07:34:57] -90: -90: **** -90: Invariant Violation -90: molzip: bond info already exists for end atom with label:1 -90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -90: Failed Expression: !bond.b -90: **** -90: -90: [07:34:57] Incomplete atom labelling, cannot make bond -90: [07:34:57] Incomplete atom labelling, cannot make bond -90: [07:34:57] Incomplete atom labelling, cannot make bond -90: [07:34:57] -90: -90: **** -90: Invariant Violation -90: molzip: bond info already exists for end atom with label:1 -90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -90: Failed Expression: !bond.b -90: **** -90: -100: [07:34:57] done -100: [07:34:57] ------------------------------------- -100: [07:34:57] Test Issue262: problems with Crippen calculation from pickles. -100: [07:34:57] done -100: [07:34:57] ------------------------------------- -100: [07:34:57] Test AMW calculation. -100: [07:34:57] done -100: [07:34:57] ------------------------------------- -100: [07:34:57] Test Exact MW calculation. -100: [07:34:57] done -100: [07:34:57] ------------------------------------- -100: [07:34:57] Test Labute ASA descriptors. -100: [07:34:57] done -100: [07:34:57] ------------------------------------- -100: [07:34:57] Test TPSA descriptors. -101: [07:34:57] ---------------------------- -101: start test autocorr2D -103: [07:34:57] ------------------------------------- -103: [07:34:57] Basic BCUT tests. -76: [07:34:57] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -76: [07:34:57] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas - 64/223 Test #89: testChemTransforms ..................... Passed 0.09 sec - 65/223 Test #102: testATF ................................ Passed 0.03 sec -test 106 - Start 106: testRDFcustom - -106: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom -106: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -106: Test timeout computed to be: 1500 -test 107 - Start 107: testRDF - -107: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF -107: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -107: Test timeout computed to be: 1500 -65: [07:34:57] Finished: testGetItemText() -65: [07:34:57] ----------------------------------------- +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testTDTSupplier3() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -90: [07:34:57] Incomplete atom labelling, cannot make bond -90: [07:34:57] -90: -90: **** -90: Invariant Violation -90: molzip: bond info already exists for end atom with label:1 -90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -90: Failed Expression: !bond.b -90: **** -90: -90: [07:34:57] -90: -90: **** -90: Invariant Violation -90: molzip: zipped Bond already exists, perhaps labels are duplicated -90: Violation occurred on line 742 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -90: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) -90: **** -90: -103: [07:34:57] done -103: [07:34:57] ------------------------------------- -103: [07:34:57] Larger BCUT tests. -76: [07:34:57] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -76: [07:34:57] Failed to parse XML fragment 5 node: b attribute: Order: 5 -76: =============================================================================== -76: All tests passed (252 assertions in 4 test cases) -76: -82: [07:34:57] mapped atoms in the reactants were not mapped in the products. -82: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 -105: [07:34:57] ------------------------------------- -105: [07:34:57] Basic PBF tests. - 66/223 Test #76: cdxmlParserCatchTest ................... Passed 0.19 sec -test 108 - Start 108: testMORSE - -108: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE -108: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -108: Test timeout computed to be: 1500 -65: [07:34:57] Finished: testForwardSDSupplier() -65: [07:34:57] ----------------------------------------- +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testSDSupplierFromText() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testMissingCRSDSupplier() -65: [07:34:57] ----------------------------------------- +65: [04:03:46] ----------------------------------------- +65: [04:03:46] ERROR: Problems encountered parsing data fields +65: [04:03:46] ERROR: moving to the beginning of the next molecule +65: [04:03:46] ERROR: Problems encountered parsing data fields +65: [04:03:46] ERROR: moving to the beginning of the next molecule +65: [04:03:46] Spurious data before the first property will be ignored +65: [04:03:46] Property will be truncated after the first blank line +65: [04:03:46] Property will be truncated after the first blank line +65: [04:03:46] Property will be truncated after the first blank line +65: [04:03:46] Finished: testSDSupplierStrLax1() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testIssue3482695() -65: [07:34:57] ----------------------------------------- +65: [04:03:46] ----------------------------------------- +65: [04:03:46] ERROR: Problems encountered parsing data fields +65: [04:03:46] ERROR: moving to the beginning of the next molecule +65: [04:03:46] Property will be truncated after the first blank line +65: [04:03:46] Finished: testSDSupplierStrLax2() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -90: =============================================================================== -90: All tests passed (667 assertions in 7 test cases) -90: -27: ...[07:34:57] Molecule does not have explicit Hs. Consider calling AddHs() - 67/223 Test #90: chemTransformsTestCatch ................ Passed 0.11 sec -test 109 - Start 109: test3D +65: [04:03:46] ----------------------------------------- +65: [04:03:46] ERROR: Problems encountered parsing data fields +65: [04:03:46] ERROR: moving to the beginning of the next molecule +test 74 + Start 74: testPropertyLists -109: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D -109: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -109: Test timeout computed to be: 1500 -65: [07:34:57] ERROR: Cannot convert 'foo' to unsigned int on line 557 -65: [07:34:57] ERROR: moving to the beginning of the next molecule -65: [07:34:57] Finished: testIssue3525673() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testBlankLinesInProps() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testSkipLines() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testGitHub23() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testGitHub88() -65: [07:34:57] ----------------------------------------- -65: -65: [07:34:57] ----------------------------------------- -27: [07:34:57] -27: -27: **** -27: Invariant Violation -27: bad direction in linearSearch -27: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h -27: Failed Expression: status >= 0 -27: **** -27: -104: =>start test EEM -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: 0 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -96: Warning: molecule failed filter -96: Warning: molecule failed filter: reason hzone_phenol_A(479) -96: v = { -96: 0,23}, -96: 1,22}, -96: 2,20}, -96: 3,19}, -96: 4,25}, -96: 5,24}, -96: 6,18}, -96: 7,17}, -96: 8,16}, -96: 9,21}, -96: } -96: match = { -96: 0,23}, -96: 1,22}, -96: 2,20}, -96: 3,19}, -96: 4,25}, -96: 5,24}, -96: 6,18}, -96: 7,17}, -96: 8,16}, -96: 9,21}, -96: } -96: Warning: molecule failed filter -96: Warning: molecule failed filter: reason cyano_imine_B(17) -96: v = { -96: 0,11}, -96: 1,12}, -96: 2,13}, -96: 3,14}, -96: 4,15}, -96: 5,10}, -96: 6,9}, -96: 7,8}, -96: 8,7}, -96: 9,6}, -96: 10,5}, -96: 11,17}, -96: 12,16}, -96: } -96: match = { -96: 0,11}, -96: 1,12}, -96: 2,13}, -96: 3,14}, -96: 4,15}, -96: 5,10}, -96: 6,9}, -96: 7,8}, -96: 8,7}, -96: 9,6}, -96: 10,5}, -96: 11,17}, -96: 12,16}, -96: } -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -93: Finished -93: ----------------------- -93: Path retrieval -93: Finished -93: ----------------------- -93: Path retrieval2 -93: Finished -93: ----------------------- -93: Unique Subgraph retrieval -93: Finished -93: ----------------------- -93: testUniqueSubgraphs2 -96: Warning: molecule failed filter -84: 30000000 30000000 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -96: Warning: molecule failed filter: reason keto_keto_gamma(5) -96: v = { -96: 0,0}, -96: 1,1}, -96: 2,2}, -96: 3,4}, -96: 4,5}, -96: 5,6}, -96: 6,7}, -96: 7,8}, -96: 8,9}, -96: 9,14}, -96: 10,15}, -96: 11,16}, -96: } -96: match = { -96: 0,0}, -96: 1,1}, -96: 2,2}, -96: 3,4}, -96: 4,5}, -96: 5,6}, -96: 6,7}, -96: 7,8}, -96: 8,9}, -96: 9,14}, -96: 10,15}, -96: 11,16}, -96: } -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -82: [07:34:57] product atom-mapping number 17 not found in reactants. -82: [07:34:57] product atom-mapping number 18 not found in reactants. -82: [07:34:57] mapped atoms in the reactants were not mapped in the products. -82: unmapped numbers are: 12 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -65: [07:34:57] Finished: testGitHub2285() -65: [07:34:57] ----------------------------------------- +74: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists +74: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +74: Test timeout computed to be: 1500 +65: [04:03:46] ERROR: Problems encountered parsing data fields +65: [04:03:46] ERROR: moving to the beginning of the next molecule +65: [04:03:46] Spurious data before the first property will be ignored +65: [04:03:46] Property will be truncated after the first blank line +65: [04:03:46] Property will be truncated after the first blank line +65: [04:03:46] Property will be truncated after the first blank line +65: [04:03:46] Finished: testSDSupplierFromTextStrLax1() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -65: [07:34:57] ERROR: Smiles parse error on line 1 -65: [07:34:57] ERROR: Cannot create molecule from : 'c1ccccc' -65: [07:34:57] SMILES Parse Error: extra open parentheses for input: 'C(C' -4: dynamic boost any:0.355241 s -65: [07:34:57] ERROR: Smiles parse error on line 3 -65: [07:34:57] ERROR: Cannot create molecule from : 'C(C' -65: [07:34:57] Explicit valence for atom # 1 C, 5, is greater than permitted -65: [07:34:57] ERROR: Could not sanitize molecule on line 5 -65: [07:34:57] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -65: [07:34:57] Explicit valence for atom # 1 F, 2, is greater than permitted -65: [07:34:57] ERROR: Could not sanitize molecule ending on line 21 -65: [07:34:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -65: [07:34:57] Explicit valence for atom # 1 F, 2, is greater than permitted -65: [07:34:57] ERROR: Could not sanitize molecule ending on line 21 -65: [07:34:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -65: [07:34:57] Explicit valence for atom # 1 F, 2, is greater than permitted -65: [07:34:57] ERROR: Could not sanitize molecule ending on line 21 -65: [07:34:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -65: [07:34:57] ERROR: Atom line too short: ' -9.6' on line 28 -65: [07:34:57] ERROR: moving to the beginning of the next molecule -65: [07:34:57] Explicit valence for atom # 1 F, 2, is greater than permitted -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -65: [07:34:57] ERROR: Could not sanitize molecule ending on line 21 -65: [07:34:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -65: [07:34:57] ERROR: Atom line too short: ' -9.6' on line 28 -65: [07:34:57] ERROR: moving to the beginning of the next molecule -65: [07:34:57] Finished: testGitHub2479() -65: [07:34:57] ----------------------------------------- +65: [04:03:46] ----------------------------------------- +65: [04:03:46] ERROR: Problems encountered parsing data fields +65: [04:03:46] ERROR: moving to the beginning of the next molecule +65: [04:03:46] Property will be truncated after the first blank line +65: [04:03:46] Finished: testSDSupplierFromTextStrLax2() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testIssue265() +65: [04:03:46] ----------------------------------------- 65: -65: **** -65: Invariant Violation -65: bad chiral bond -65: Violation occurred on line 164 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -65: Failed Expression: bnd -65: **** +65: [04:03:46] ----------------------------------------- +65: [04:03:46] ERROR: End of data field name not found +65: [04:03:46] ERROR: moving to the beginning of the next molecule +65: [04:03:46] Explicit valence for atom # 0 F, 2, is greater than permitted +65: [04:03:46] ERROR: Could not sanitize molecule ending on line 16 +65: [04:03:46] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +65: [04:03:46] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +65: [04:03:46] ERROR: moving to the beginning of the next molecule +65: [04:03:46] ERROR: Bond line too short: 'M END' on line 18 +65: [04:03:46] ERROR: moving to the beginning of the next molecule +65: [04:03:46] Finished: testSDErrorHandling() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] Finished: testGitHub2881() -65: [07:34:57] ----------------------------------------- +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testIssue381() +65: [04:03:46] ----------------------------------------- 65: -65: [07:34:57] ----------------------------------------- -65: [07:34:57] Finished: testGitHub3517() -65: [07:34:57] ----------------------------------------- +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testSetStreamIndices() +65: [04:03:46] ----------------------------------------- 65: -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [07:34:57] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -109: [07:34:57] ------------------------------------- -109: [07:34:57] Basic PMI tests. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 68/223 Test #65: testMolSupplier ........................ Passed 0.28 sec -test 110 - Start 110: testWHIM - -110: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM -110: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -110: Test timeout computed to be: 1500 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [07:34:57] bond with order 0 found on line 11. This is not part of the MDL specification. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -68: [07:34:57] bond with order 0 found on line 16. This is not part of the MDL specification. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -60: [07:34:57] Warning: stereochemistry around double bond may be incorrect in depiction. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +65: [04:03:46] ----------------------------------------- +60: [04:03:46] Warning: stereochemistry around double bond may be incorrect in depiction. 63: Test 63: 63: lostStereoAnd.sdf @@ -17141,27 +16026,17 @@ 63: 63: MulticenterSgroup.mrv 63: -63: [07:34:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -63: [07:34:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -100: [07:34:57] done -100: [07:34:57] ------------------------------------- -100: [07:34:57] Test Lipinski parameters. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 69/223 Test #68: testMolWriter .......................... Passed 0.29 sec -test 111 - Start 111: testGETAWAY - -111: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY -111: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -111: Test timeout computed to be: 1500 +63: [04:03:46] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +63: [04:03:46] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +65: [04:03:46] Finished: testMixIterAndRandom() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +65: build: +65: [04:03:46] Finished: testRemoveHs() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- 63: Test 63: 63: GenericSgroup.mrv @@ -17194,7 +16069,7 @@ 63: 63: MarvinBadMissingMolID.mrv 63: -63: [07:34:57] +63: [04:03:46] 63: 63: **** 63: Test Assert @@ -17240,17 +16115,197 @@ 63: MarvinBadMissingBondOrder.mrv 63: 63: bond must have one of: order, queryType, or convention in MRV File + 55/223 Test #72: testExtendedStereoParsing .............. Passed 0.11 sec +test 75 + Start 75: XYZFileParserCatchTest + +75: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest +75: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +75: Test timeout computed to be: 1500 +73: Randomness seeded to: 565814800 +73: [04:03:46] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +73: [04:03:46] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +73: [04:03:46] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +73: [04:03:46] SGroup 1 is invalid and will be ignored +73: [04:03:46] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +73: [04:03:46] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +73: [04:03:46] SGroup 1 is invalid and will be ignored +73: [04:03:46] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +73: [04:03:46] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +73: [04:03:46] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +73: [04:03:46] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +73: [04:03:46] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +73: [04:03:46] SGroup 1 is invalid and will be ignored +73: [04:03:46] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +73: [04:03:46] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +73: [04:03:46] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +73: [04:03:46] SGroup 1 is invalid and will be ignored +73: [04:03:46] SGroup 3 referenced on line 40 not found. +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: no bonds +73: Violation occurred on line 139 in file ./Code/GraphMol/SubstanceGroup.cpp +73: Failed Expression: !d_bonds.empty() +73: **** +73: +73: [04:03:46] SGroup 3 referenced on line 40 not found. +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: no bonds +73: Violation occurred on line 139 in file ./Code/GraphMol/SubstanceGroup.cpp +73: Failed Expression: !d_bonds.empty() +73: **** +73: +73: [04:03:46] no bonds +73: [04:03:46] SGroup 1 is invalid and will be ignored +73: [04:03:46] SGroup line too short: 'M SBV 1 6' on line 42 +73: [04:03:46] SGroup 1 is invalid and will be ignored +73: [04:03:46] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +73: [04:03:46] SGroup 2 is invalid and will be ignored +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: bookmark not found +73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp +73: Failed Expression: (lu != d_bondBookmarks.end()) +73: **** +73: +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: bookmark not found +73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp +73: Failed Expression: (lu != d_bondBookmarks.end()) +73: **** +73: +73: [04:03:46] bookmark not found +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: bond is not part of the SubstanceGroup +73: Violation occurred on line 158 in file ./Code/GraphMol/SubstanceGroup.cpp +73: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() +73: **** +73: +73: [04:03:46] bond is not part of the SubstanceGroup +73: [04:03:46] SGroup 2 is invalid and will be ignored +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: bookmark not found +73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp +73: Failed Expression: (lu != d_atomBookmarks.end()) +73: **** +73: +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: bookmark not found +73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp +73: Failed Expression: (lu != d_atomBookmarks.end()) +73: **** +73: +73: [04:03:46] bookmark not found +73: [04:03:46] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +73: [04:03:46] SGroup 2 is invalid and will be ignored +73: [04:03:46] WARNING: final character of V3000 array is not ')' +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: bookmark not found +73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp +73: Failed Expression: (lu != d_bondBookmarks.end()) +73: **** +73: +73: [04:03:46] WARNING: final character of V3000 array is not ')' +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: bookmark not found +73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp +73: Failed Expression: (lu != d_bondBookmarks.end()) +73: **** +73: +73: [04:03:46] bookmark not found +73: [04:03:46] SGroup 1 is invalid and will be ignored +73: [04:03:46] WARNING: final character of V3000 array is not ')' +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: bookmark not found +73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp +73: Failed Expression: (lu != d_atomBookmarks.end()) +73: **** +73: +73: [04:03:46] WARNING: final character of V3000 array is not ')' +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: bookmark not found +73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp +73: Failed Expression: (lu != d_atomBookmarks.end()) +73: **** +73: +73: [04:03:46] bookmark not found +73: [04:03:46] SGroup 1 is invalid and will be ignored +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: bookmark not found +73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp +73: Failed Expression: (lu != d_bondBookmarks.end()) +73: **** +73: +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: bookmark not found +73: Violation occurred on line 271 in file ./Code/GraphMol/ROMol.cpp +73: Failed Expression: (lu != d_bondBookmarks.end()) +73: **** +73: +73: [04:03:46] bookmark not found +73: [04:03:46] SGroup 2 is invalid and will be ignored +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: bookmark not found +73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp +73: Failed Expression: (lu != d_atomBookmarks.end()) +73: **** +73: +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: bookmark not found +73: Violation occurred on line 249 in file ./Code/GraphMol/ROMol.cpp +73: Failed Expression: (lu != d_atomBookmarks.end()) +73: **** +73: +73: [04:03:46] bookmark not found +73: [04:03:46] SGroup 2 is invalid and will be ignored 63: Test 63: 63: MarvinBadMissingSruMolID.mrv 63: 63: Expected a molID in MRV file -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadMissingSruID.mrv @@ -17272,7 +16327,6 @@ 63: MarvinBadSruAtomRef.mrv 63: 63: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSruID.mrv @@ -17286,25 +16340,16 @@ 63: MarvinBadSruAtomRef.mrv 63: 63: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSruAtomRef.mrv 63: 63: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -79: done -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -79: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -79: processing2 -79: launch2 :0 63: Test 63: 63: MarvinBadSruConnect.mrv 63: 63: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file -79: launch2 :1 -79: launch2 :2 -79: launch2 :3 63: Test 63: 63: MarvinBadSupAttachAtom.mrv @@ -17315,124 +16360,204 @@ 63: MarvinBadSupAttachBond.mrv 63: 63: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -4: static RDAny:0.050281 s -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSupAttachOrder.mrv 63: 63: Order for an AttachmentPoint definition must be an integer in MRV file -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSupAttachAtom.mrv 63: 63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSupAttachAtom.mrv 63: 63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSupAttachAtom.mrv 63: 63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSupMissingAttachBond.mrv 63: 63: No attachment point found for bond to the condensed atom in a superatomSgroup -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 63: Test 63: 63: MarvinBadSupMissingAttachOrder.mrv 63: 63: Expected atom, order and bond, for an AttachmentPoint definition in MRV file -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -82: [07:34:57] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -82: [07:34:57] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -82: -82: [07:34:57] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -82: ------------- -82: CCOc1ccccc1 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -79: done -79: preprocessing 3 -91: Randomness seeded to: 3317144408 -91: =============================================================================== -91: All tests passed (93 assertions in 13 test cases) -91: -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -79: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 -79: processing3 -79: launch3 :0 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 70/223 Test #91: tautomerQueryTestCatch ................. Passed 0.21 sec -test 112 - Start 112: testAUTOCORR3D +65: [04:03:46] Finished: testGetItemText() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +73: [04:03:46] Explicit valence for atom # 2 O, 3, is greater than permitted +73: [04:03:46] Explicit valence for atom # 1 O, 3, is greater than permitted +73: [04:03:46] Explicit valence for atom # 1 C, 5, is greater than permitted +33: [04:03:46] Maximum BFS search size exceeded. +33: This is likely due to a highly symmetric fused ring system. +73: [04:03:46] sanitize [04:03:46] UNK: [04:03:46] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +27: ... +27: ---------------------------------------------------------------------- +27: Ran 12 tests in 0.746s +27: +27: OK +74: Randomness seeded to: 3981102785 +74: =============================================================================== +74: All tests passed (95 assertions in 4 test cases) +74: +65: [04:03:46] Finished: testForwardSDSupplier() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testMissingCRSDSupplier() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testIssue3482695() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- + 56/223 Test #74: testPropertyLists ...................... Passed 0.13 sec +test 76 + Start 76: cdxmlParserCatchTest -112: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D -112: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -112: Test timeout computed to be: 1500 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -79: launch3 :1 -79: launch3 :2 -79: launch3 :3 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 71/223 Test #60: testDepictor ........................... Passed 0.39 sec -test 113 - Start 113: testCoulombMat +76: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest +76: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +76: Test timeout computed to be: 1500 +65: [04:03:46] ERROR: Cannot convert 'foo' to unsigned int on line 557 +65: [04:03:46] ERROR: moving to the beginning of the next molecule +65: [04:03:46] Finished: testIssue3525673() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testBlankLinesInProps() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testSkipLines() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testGitHub23() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testGitHub88() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +73: [04:03:46] skipping block at line 7: 'BEGIN ATOM' +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: no stream +73: Violation occurred on line 144 in file ./Code/GraphMol/FileParsers/SDMolSupplier.cpp +73: Failed Expression: dp_inStream +73: **** +73: +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: no stream +73: Violation occurred on line 179 in file ./Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp +73: Failed Expression: dp_inStream +73: **** +73: +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: no stream +73: Violation occurred on line 427 in file ./Code/GraphMol/FileParsers/SmilesMolSupplier.cpp +73: Failed Expression: dp_inStream +73: **** +73: +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: no stream +73: Violation occurred on line 274 in file ./Code/GraphMol/FileParsers/TDTMolSupplier.cpp +73: Failed Expression: dp_inStream +73: **** +73: +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: no stream +73: Violation occurred on line 515 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +73: Failed Expression: dp_sInStream != nullptr +73: **** +73: +73: [04:03:46] Found a SCD/SED line with missing/empty SDT specification at line 21 +73: [04:03:46] Found a SCD/SED line with missing/empty SDT specification at line 20 +73: [04:03:46] +73: +73: **** +73: Post-condition Violation +73: Element '' not found +73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +73: Failed Expression: anum > -1 +73: **** +73: +73: [04:03:46] BEGIN SGROUP line not found on line 14 +75: Randomness seeded to: 446132542 +75: =============================================================================== +75: All tests passed (100 assertions in 2 test cases) +75: + 57/223 Test #75: XYZFileParserCatchTest ................. Passed 0.09 sec +test 77 + Start 77: molfileStereoCatchTest -113: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat -113: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -113: Test timeout computed to be: 1500 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +77: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest +77: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +77: Test timeout computed to be: 1500 +73: [04:03:46] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +73: [04:03:46] END SGROUP line not found on line 14 +73: [04:03:46] END SGROUP line not found on line 14 +73: [04:03:46] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +73: [04:03:46] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +73: [04:03:46] +73: +73: **** +73: Range Error +73: idx +73: Violation occurred on line 328 in file ./Code/GraphMol/ROMol.cpp +73: Failed Expression: 99 < 9 +73: **** +73: +73: [04:03:46] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +73: [04:03:46] Multiple ATTCHPT values for atom 2 on line 9 +73: [04:03:46] Found a SCD/SED line with missing/empty SDT specification at line 12 +73: [04:03:46] SMARTS Parse Error: syntax error while parsing: [#6;R +73: [04:03:46] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +73: [04:03:46] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +73: [04:03:46] Skipping empty SMARTS value for SMARTSQ. +73: [04:03:46] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +73: [04:03:46] Found a SCD/SED line with missing/empty SDT specification at line 12 +73: [04:03:46] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +73: [04:03:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [04:03:46] WARNING: Skipping property bar because the value includes an illegal blank line +4: dynamic RDValue:0.079281 s +4: deleted! +4: [04:03:46] ------------------------------------- +4: [04:03:46] Testing String Pickle Roundtrips. +4: [04:03:46] done +4: [04:03:46] ------------------------------------- +4: [04:03:46] Testing conversion of vect to string. +4: [04:03:46] done +4: [04:03:46] ------------------------------------- +4: [04:03:46] Testing returning const references. +4: [04:03:46] any cast +4: [04:03:46] done: 0.001593 300000 +4: [04:03:46] copy 63: Test 63: 63: marvin03.mrv @@ -17477,53 +16602,140 @@ 63: 63: EmptyRxn.mrv 63: -63: [07:34:57] initialization failed -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: 100 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: ===================== Testing CoulombMat ======================= -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -113: CM test 1 mat Done -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 72/223 Test #113: testCoulombMat ......................... Passed 0.04 sec -test 114 - Start 114: descriptorsTestCatch +63: [04:03:46] initialization failed +4: [04:03:46] done: 0.001392 300000 +4: [04:03:46] ref +4: [04:03:46] done: 0.001507 300000 +4: [04:03:46] dict +73: [04:03:46] WARNING: Skipping property baz because the value includes an illegal blank line +73: [04:03:46] WARNING: Skipping property bletch +73: nope because the name includes a newline +73: [04:03:46] WARNING: Skipping property bletch +73: nope2 because the name includes a newline +73: [04:03:46] +73: +73: **** +73: Post-condition Violation +73: Element 'QQQ' not found +73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +73: Failed Expression: anum > -1 +73: **** +73: +73: [04:03:46] +73: +73: **** +73: Post-condition Violation +73: Element 'QQQ' not found +73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +73: Failed Expression: anum > -1 +73: **** +73: +73: [04:03:46] +73: +73: **** +73: Post-condition Violation +73: Element 'QQQ' not found +73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +73: Failed Expression: anum > -1 +73: **** +73: +73: [04:03:46] +73: +73: **** +73: Post-condition Violation +73: Element 'QQQ' not found +73: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +73: Failed Expression: anum > -1 +73: **** +73: +73: [04:03:46] atom 3 has a negative isotope value. line: 15 +65: [04:03:46] Finished: testGitHub2285() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +65: [04:03:46] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +65: [04:03:46] ERROR: Smiles parse error on line 1 +65: [04:03:46] ERROR: Cannot create molecule from : 'c1ccccc' +65: [04:03:46] SMILES Parse Error: extra open parentheses for input: 'C(C' +65: [04:03:46] ERROR: Smiles parse error on line 3 +65: [04:03:46] ERROR: Cannot create molecule from : 'C(C' +65: [04:03:46] Explicit valence for atom # 1 C, 5, is greater than permitted +65: [04:03:46] ERROR: Could not sanitize molecule on line 5 +65: [04:03:46] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +65: [04:03:46] Explicit valence for atom # 1 F, 2, is greater than permitted +65: [04:03:46] ERROR: Could not sanitize molecule ending on line 21 +65: [04:03:46] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +65: [04:03:46] Explicit valence for atom # 1 F, 2, is greater than permitted +65: [04:03:46] ERROR: Could not sanitize molecule ending on line 21 +65: [04:03:46] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +65: [04:03:46] Explicit valence for atom # 1 F, 2, is greater than permitted +65: [04:03:46] ERROR: Could not sanitize molecule ending on line 21 +65: [04:03:46] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +65: [04:03:46] ERROR: Atom line too short: ' -9.6' on line 28 +65: [04:03:46] ERROR: moving to the beginning of the next molecule +65: [04:03:46] Explicit valence for atom # 1 F, 2, is greater than permitted +65: [04:03:46] ERROR: Could not sanitize molecule ending on line 21 +65: [04:03:46] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +65: [04:03:46] ERROR: Atom line too short: ' -9.6' on line 28 +65: [04:03:46] ERROR: moving to the beginning of the next molecule +65: [04:03:46] Finished: testGitHub2479() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +65: [04:03:46] +65: +65: **** +65: Invariant Violation +65: bad chiral bond +65: Violation occurred on line 164 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +65: Failed Expression: bnd +65: **** +65: + 58/223 Test #60: testDepictor ........................... Passed 0.77 sec +test 78 + Start 78: connectTheDotsTest -114: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch -114: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -114: Test timeout computed to be: 1500 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +78: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest +78: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +78: Test timeout computed to be: 1500 +4: [04:03:46] done: 0.004147 300000 +4: [04:03:46] ref with hasVal +4: [04:03:46] done: 0.002041 300000 +4: [04:03:46] done +4: [04:03:46] ------------------------------------- +4: [04:03:46] Testing dict update. +4: [04:03:46] done +4: deleted! +4: deleted! +4: deleted! +4: deleted! +4: deleted! +4: deleted! +65: [04:03:46] Finished: testGitHub2881() +65: [04:03:46] ----------------------------------------- +65: +65: [04:03:46] ----------------------------------------- +65: [04:03:46] Finished: testGitHub3517() +65: [04:03:46] ----------------------------------------- +65: +73: [04:03:46] +73: +73: **** +73: Invariant Violation +73: bad prop value +73: Violation occurred on line 158 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +73: Failed Expression: nSwaps < 2 +73: **** +73: +73: [04:03:46] +73: +73: **** +73: Pre-condition Violation +73: no input stream +73: Violation occurred on line 480 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +73: Failed Expression: dp_sInStream +73: **** +73: 63: Test 63: 63: RxnNoCoords.mrv @@ -17608,224 +16820,957 @@ 63: 63: Smiles1 63: -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 73/223 Test #63: testMrvToMol ........................... Passed 0.43 sec -test 115 - Start 115: pyMolDescriptors +77: Randomness seeded to: 3116246925 +77: [04:03:46] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +77: [04:03:46] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +77: [04:03:46] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +77: [04:03:46] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +77: [04:03:46] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 2 ignored +77: =============================================================================== +77: All tests passed (142 assertions in 6 test cases) +77: + 59/223 Test #4: testDict ............................... Passed 1.77 sec + 60/223 Test #63: testMrvToMol ........................... Passed 0.78 sec + 61/223 Test #65: testMolSupplier ........................ Passed 0.74 sec +test 79 + Start 79: testSubstructMatch -115: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" -115: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap -115: Test timeout computed to be: 1500 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -100: [07:34:57] done -100: [07:34:57] ------------------------------------- -100: [07:34:57] Test VSA descriptors. - 74/223 Test #96: filterCatalogTest ...................... Passed 0.28 sec -test 116 - Start 116: pyMolDescriptors3D +79: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +79: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct +79: Test timeout computed to be: 1500 +test 80 + Start 80: substructTestCatch -116: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/test3D.py" -116: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap -116: Test timeout computed to be: 1500 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -100: [07:34:57] done -100: [07:34:57] ------------------------------------- -100: [07:34:57] Test molecular formula calculation. -100: [07:34:57] done -100: [07:34:57] ------------------------------------- -100: [07:34:57] Test Issue 3415534. -100: [07:34:57] done -100: [07:34:57] ------------------------------------- -100: [07:34:57] Test Issue3433771: Bad definition for Crippen atom type O11. -100: [07:34:57] done -100: [07:34:57] ------------------------------------- -100: [07:34:57] Test multithreading -100: reading molecules -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +80: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch +80: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct +80: Test timeout computed to be: 1500 +test 81 + Start 81: testGenericGroups + +81: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups +81: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups +81: Test timeout computed to be: 1500 +76: Randomness seeded to: 17259024 +76: [04:03:46] Invalid or missing fragment id from CDXML fragment, assigning new one... +76: [04:03:46] Explicit valence for atom # 3 N, 4, is greater than permitted +76: [04:03:46] CDXMLParser: failed sanitizing skipping fragment 32 +76: [04:03:46] Bad bond in CDXML skipping fragment 58... +76: [04:03:46] Invalid or missing fragment id from CDXML fragment, assigning new one... +76: [04:03:46] Bad bond in CDXML skipping fragment 58... +79: ----------------- Test 1 +79: Done +79: +79: ----------------- Test 2 +79: Done +79: +79: ----------------- Test 3 +79: Done +79: +79: ----------------- Test 4 +79: Done +79: +79: ----------------- Test 5 +79: Done +79: +79: ----------------- Test 5 QueryRoot +79: Done +79: +79: ----------------- Test 6 (Issue71 related) +79: Done +79: +79: ----------------- Testing serial numbers on recursive queries +79: Done +79: +79: [04:03:46] ------------------------------------- +79: [04:03:46] Test multithreading +79: reading molecules + 62/223 Test #77: molfileStereoCatchTest ................. Passed 0.14 sec +test 82 + Start 82: testReaction + +82: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction +82: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +82: Test timeout computed to be: 1500 +78: Randomness seeded to: 1928374499 +78: =============================================================================== +78: All tests passed (8 assertions in 1 test case) +78: + 63/223 Test #78: connectTheDotsTest ..................... Passed 0.13 sec +test 83 + Start 83: testReactionFingerprints + +83: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints +83: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +83: Test timeout computed to be: 1500 + 64/223 Test #27: pyForceFieldConstraints ................ Passed 1.64 sec +test 84 + Start 84: testEnumeration + +84: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration +84: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +84: Test timeout computed to be: 1500 +79: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +79: processing +79: launch :0 +79: launch :1 +79: launch :2 +79: launch :3 +76: [04:03:47] WARNING: not removing hydrogen atom without neighbors +76: [04:03:47] WARNING: not removing hydrogen atom without neighbors +76: [04:03:47] WARNING: not removing hydrogen atom without neighbors +76: [04:03:47] WARNING: not removing hydrogen atom without neighbors +83: [04:03:47] ------------------------------------- +83: [04:03:47] Test Reaction StructuralFingerprint +76: [04:03:47] WARNING: not removing hydrogen atom without neighbors +76: [04:03:47] WARNING: not removing hydrogen atom without neighbors +76: [04:03:47] WARNING: not removing hydrogen atom without neighbors +68: [04:03:47] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +76: [04:03:47] WARNING: not removing hydrogen atom without neighbors +76: [04:03:47] WARNING: not removing hydrogen atom without neighbors +82: smi: O=C1CNC(=O)CN1 +82: 1: O=C1CNC(=O)CN1 +82: 2: COOC +82: [04:03:47] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +82: [04:03:47] 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]' +82: O=C1CNC(=O)CN1 +76: [04:03:47] WARNING: not removing hydrogen atom without neighbors +76: [04:03:47] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. +68: [04:03:47] bond with order 0 found on line 11. This is not part of the MDL specification. +68: [04:03:47] bond with order 0 found on line 16. This is not part of the MDL specification. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] mapped atoms in the reactants were not mapped in the products. +82: unmapped numbers are: 4 +73: [04:03:47] ERROR: molecules without atoms cannot be exported to Maestro files. +73: [04:03:47] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +73: [04:03:47] ERROR: the mol cannot be kekulized, and will not be written to the output file. +73: [04:03:47] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. +82: [04:03:47] atom 0 in product 0 has multiple charge specifications. +82: mass: 15.0001 +73: [04:03:47] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +73: [04:03:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [04:03:47] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +73: [04:03:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +82: Oc1ccccn1 +82: Oc1ccc[nH]1 +56: Randomness seeded to: 3422590202 +56: =============================================================================== +56: All tests passed (1902 assertions in 21 test cases) +56: + 65/223 Test #56: cxsmilesTest ........................... Passed 1.06 sec +test 85 + Start 85: rxnTestCatch + +85: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch +85: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +85: Test timeout computed to be: 1500 +73: =============================================================================== +73: All tests passed (1311 assertions in 87 test cases) +73: +83: [04:03:47] ------------------------------------- +83: [04:03:47] Test Reaction DifferenceFingerprint +82: [04:03:47] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +82: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +82: [04:03:47] SMARTS Parse Error: syntax error while parsing: ([C:2] +82: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +82: [04:03:47] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +82: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +82: [04:03:47] SMARTS Parse Error: syntax error while parsing: [C:2]) +82: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' + 66/223 Test #73: fileParsersCatchTest ................... Passed 0.44 sec +test 86 + Start 86: pyChemReactions + +86: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" +86: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +86: Test timeout computed to be: 1500 +82: [04:03:47] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +82: [04:03:47] 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]' +82: [04:03:47] reactant 2 has no mapped atoms. +82: [04:03:47] >> Atoms within one molecule have different RXN roles. +82: [04:03:47] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +82: [04:03:47] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +82: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +82: [04:03:47] SMARTS Parse Error: syntax error while parsing: ([C:2] +82: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +82: [04:03:47] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +82: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +82: [04:03:47] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +82: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +82: [04:03:47] reactant 0 has no mapped atoms. +82: [04:03:47] reactant 1 has no mapped atoms. +82: [04:03:47] reactant 3 has no mapped atoms. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 4 found multiple times. +82: [04:03:47] product atom-mapping number 5 found multiple times. +82: [04:03:47] product atom-mapping number 6 found multiple times. +82: [04:03:47] product atom-mapping number 7 found multiple times. +82: [04:03:47] product atom-mapping number 8 found multiple times. +82: [04:03:47] product atom-mapping number 12 found multiple times. +82: [04:03:47] product atom-mapping number 9 found multiple times. +82: [04:03:47] product atom-mapping number 10 found multiple times. +82: [04:03:47] product atom-mapping number 11 found multiple times. +82: [04:03:47] reactant 0 has no mapped atoms. +82: [04:03:47] reactant 1 has no mapped atoms. +82: [04:03:47] reactant 3 has no mapped atoms. +82: [04:03:47] reactant atom-mapping number 19 found multiple times. +82: [04:03:47] reactant atom-mapping number 25 found multiple times. +82: [04:03:47] reactant atom-mapping number 20 found multiple times. +82: [04:03:47] reactant atom-mapping number 21 found multiple times. +82: [04:03:47] reactant atom-mapping number 22 found multiple times. +82: [04:03:47] reactant atom-mapping number 23 found multiple times. +82: [04:03:47] reactant atom-mapping number 24 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +82: [04:03:47] product atom-mapping number 5 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 4 found multiple times. +82: [04:03:47] product atom-mapping number 5 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 4 found multiple times. +82: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +82: [04:03:47] product atom-mapping number 5 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 4 found multiple times. +82: [04:03:47] product atom-mapping number 5 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 4 found multiple times. +82: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 4 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 4 found multiple times. +82: F[C@@](Cl)(Br)O[C@](F)(Cl)Br +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 4 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 4 found multiple times. +82: F[C@](Cl)(Br)O[C@](F)(Cl)Br +82: [04:03:47] product atom-mapping number 4 found multiple times. +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 4 found multiple times. +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 4 found multiple times. +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 4 found multiple times. +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] mapped atoms in the reactants were not mapped in the products. +82: unmapped numbers are: 4 +82: [04:03:47] product atom-mapping number 3 found multiple times. +82: [04:03:47] product atom-mapping number 2 found multiple times. +82: [04:03:47] product atom-mapping number 1 found multiple times. +82: [04:03:47] mapped atoms in the reactants were not mapped in the products. +82: unmapped numbers are: 4 +82: [04:03:47] product atom-mapping number 6 not found in reactants. +82: [04:03:47] product atom-mapping number 7 not found in reactants. +82: [04:03:47] product atom-mapping number 8 not found in reactants. +82: [04:03:47] product atom-mapping number 7 not found in reactants. +82: [04:03:47] product atom-mapping number 8 not found in reactants. +82: [04:03:47] product atom-mapping number 9 not found in reactants. +82: [04:03:47] product atom-mapping number 10 not found in reactants. +82: [04:03:47] mapped atoms in the reactants were not mapped in the products. +82: unmapped numbers are: 6 +82: [04:03:47] product atom-mapping number 7 not found in reactants. +82: [04:03:47] product atom-mapping number 8 not found in reactants. +82: [04:03:47] product atom-mapping number 9 not found in reactants. +82: [04:03:47] product atom-mapping number 10 not found in reactants. +82: [04:03:47] mapped atoms in the reactants were not mapped in the products. +82: unmapped numbers are: 6 + 67/223 Test #83: testReactionFingerprints ............... Passed 0.12 sec +test 87 + Start 87: pyChemReactionEnumerations + +87: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" +87: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +87: Test timeout computed to be: 1500 +82: 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] +82: 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] +76: [04:03:47] Incomplete atom labelling, cannot make bond +76: [04:03:47] Incomplete atom labelling, cannot make bond + 68/223 Test #68: testMolWriter .......................... Passed 0.75 sec +test 88 + Start 88: pyChemReactionSanitize + +88: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" +88: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +88: Test timeout computed to be: 1500 +85: Randomness seeded to: 799279487 +85: [04:03:47] atom 0 in product 0 has multiple charge specifications. +76: [04:03:47] Incomplete atom labelling, cannot make bond +85: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 34 +85: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 36 +85: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 38 +85: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 40 +85: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 42 +85: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 87 +85: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 89 +85: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 91 +85: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 93 +85: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 95 +82: [04:03:47] mapped atoms in the reactants were not mapped in the products. +82: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 +85: [04:03:47] mapped atoms in the reactants were not mapped in the products. +85: unmapped numbers are: 2 +85: [04:03:47] mapped atoms in the reactants were not mapped in the products. +85: unmapped numbers are: 2 +85: [04:03:47] SMARTS Parse Error: unclosed ring for input: 'CC1' +85: [04:03:47] SMILES Parse Error: unclosed ring for input: 'CC1' +85: [04:03:47] mapped atoms in the reactants were not mapped in the products. +85: unmapped numbers are: 2 +85: [04:03:47] product atom-mapping number 2 not found in reactants. +85: [04:03:47] mapped atoms in the reactants were not mapped in the products. +85: unmapped numbers are: 2 +85: [04:03:47] product atom-mapping number 2 not found in reactants. +85: [04:03:47] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +85: =============================================================================== +85: All tests passed (568 assertions in 20 test cases) +85: + 69/223 Test #85: rxnTestCatch ........................... Passed 0.14 sec +test 89 + Start 89: testChemTransforms + +89: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms +89: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms +89: Test timeout computed to be: 1500 +76: [04:03:47] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +76: [04:03:47] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +76: [04:03:47] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +76: [04:03:47] Failed to parse XML fragment 5 node: b attribute: Order: 5 +76: =============================================================================== +76: All tests passed (252 assertions in 4 test cases) +76: +82: [04:03:47] product atom-mapping number 17 not found in reactants. +82: [04:03:47] product atom-mapping number 18 not found in reactants. +82: [04:03:47] mapped atoms in the reactants were not mapped in the products. +82: unmapped numbers are: 12 + 70/223 Test #76: cdxmlParserCatchTest ................... Passed 0.44 sec +test 90 + Start 90: chemTransformsTestCatch + +90: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +90: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms +90: Test timeout computed to be: 1500 +89: 1 smi: CC +89: 1 smi: CC +89: 2 smi: CCO[C@H](N)P +89: 2 smi: CC +89: replaceSub smi1:CCP(CC)[C@@H](N)O +89: replaceSub smi1:CCNCC +89: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O +89: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O +89: [04:03:47] SMARTS Parse Error: syntax error while parsing: bar +89: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' +90: Randomness seeded to: 887590246 +90: [04:03:47] Incomplete atom labelling, cannot make bond +90: [04:03:47] +90: +90: **** +90: Invariant Violation +90: molzip: bond info already exists for end atom with label:1 +90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +90: Failed Expression: !bond.b +90: **** +90: +33: [04:03:47] Maximum BFS search size exceeded. +33: This is likely due to a highly symmetric fused ring system. +82: [04:03:47] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +82: [04:03:47] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +82: +82: [04:03:47] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +82: ------------- +82: CCOc1ccccc1 +90: [04:03:47] Incomplete atom labelling, cannot make bond +90: [04:03:47] +90: +90: **** +90: Invariant Violation +90: molzip: bond info already exists for end atom with label:1 +90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +90: Failed Expression: !bond.b +90: **** +90: + 71/223 Test #89: testChemTransforms ..................... Passed 0.18 sec +test 91 + Start 91: tautomerQueryTestCatch + +91: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch +91: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery +91: Test timeout computed to be: 1500 +90: [04:03:47] Incomplete atom labelling, cannot make bond +90: [04:03:47] +90: +90: **** +90: Invariant Violation +90: molzip: bond info already exists for end atom with label:1 +90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +90: Failed Expression: !bond.b +90: **** +90: +79: done +79: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +79: processing2 +79: launch2 :0 +79: launch2 :1 +79: launch2 :2 +79: launch2 :3 +33: F/C=C/Cl +33: [H]/C(F)=C(/[H])Cl +33: F/C=C/Cl +33: F/C=C/Cl +33: C/C(F)=C(/C)Cl +90: [04:03:47] Incomplete atom labelling, cannot make bond +90: [04:03:47] Incomplete atom labelling, cannot make bond +90: [04:03:47] Incomplete atom labelling, cannot make bond +90: [04:03:47] +90: +90: **** +90: Invariant Violation +90: molzip: bond info already exists for end atom with label:1 +90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +90: Failed Expression: !bond.b +90: **** +90: +84: 30000000 30000000 +90: [04:03:47] Incomplete atom labelling, cannot make bond +90: [04:03:47] +90: +90: **** +90: Invariant Violation +90: molzip: bond info already exists for end atom with label:1 +90: Violation occurred on line 999 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +90: Failed Expression: !bond.b +90: **** +90: +90: [04:03:47] +90: +90: **** +90: Invariant Violation +90: molzip: zipped Bond already exists, perhaps labels are duplicated +90: Violation occurred on line 742 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +90: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) +90: **** +90: +90: =============================================================================== +90: All tests passed (667 assertions in 7 test cases) +90: + 72/223 Test #90: chemTransformsTestCatch ................ Passed 0.20 sec +test 92 + Start 92: pyTautomerQuery + +92: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" +92: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap +92: Test timeout computed to be: 1500 +80: Randomness seeded to: 1367524967 +80: =============================================================================== +80: All tests passed (143 assertions in 7 test cases) +80: + 73/223 Test #80: substructTestCatch ..................... Passed 0.53 sec +test 93 + Start 93: testSubgraphs1 + +93: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 +93: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +93: Test timeout computed to be: 1500 +79: done +79: preprocessing 3 +79: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 +79: processing3 +79: launch3 :0 +79: launch3 :1 +79: launch3 :2 +79: launch3 :3 +93: ----------------------- +93: Subgraph retrieval 93: Finished 93: ----------------------- -93: testRootedSubgraphs +93: testSubgraphs2a + 74/223 Test #33: graphmolMolOpsTest ..................... Passed 2.00 sec +test 94 + Start 94: testSubgraphs2 + +94: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 +94: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +94: Test timeout computed to be: 1500 93: Finished 93: ----------------------- -93: testRootedPaths +93: testSubgraphs2 +94: ----------------------- +94: Test1: pathToSubmol +94: Finished +94: ----------------------- +94: Test2: Atom Environments +94: Finished +94: ----------------------- +94: Test 3: Atom Environments (Extension) +94: Finished +94: ----------------------- +94: Testing github Issue103: stereochemistry and pathToSubmol +94: Finished +94: ----------------------- +94: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) +94: Finished + 75/223 Test #94: testSubgraphs2 ......................... Passed 0.06 sec +test 95 + Start 95: subgraphsCatch + +95: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch +95: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +95: Test timeout computed to be: 1500 +62: ..............[04:03:47] SMILES Parse Error: syntax error while parsing: invalidsmiles +62: [04:03:47] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' +95: Randomness seeded to: 3641357308 +95: --------- +95: =============================================================================== +95: All tests passed (11 assertions in 1 test case) +95: + 76/223 Test #95: subgraphsCatch ......................... Passed 0.04 sec +test 96 + Start 96: filterCatalogTest + +96: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest +96: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog +96: Test timeout computed to be: 1500 +79: done +79: [04:03:47] done +79: [04:03:47] ------------------------------------- +79: [04:03:47] Test GitHub issue 15 +79: [04:03:47] done +79: [04:03:47] ------------------------------------- +79: [04:03:47] Test GitHub issue 409 +79: [04:03:47] done +79: [04:03:47] ------------------------------------- +79: [04:03:47] Test chiral matching +79: [04:03:47] done +79: [04:03:47] ------------------------------------- +79: [04:03:47] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +79: [04:03:47] done +79: [04:03:47] ------------------------------------- +79: [04:03:47] Test dative-bond matching +79: [04:03:47] done +79: [04:03:47] ------------------------------------- +79: [04:03:47] Test cis/trans matching +79: [04:03:47] done +79: [04:03:47] ------------------------------------- +79: [04:03:47] Test cis/trans matching part 2 +79: [04:03:47] done +79: [04:03:47] ------------------------------------- +79: [04:03:47] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +79: [04:03:47] done +86: [04:03:47] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 93: Finished -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 75/223 Test #93: testSubgraphs1 ......................... Passed 0.31 sec -test 117 - Start 117: testFingerprints +93: ----------------------- +93: Path retrieval +93: Finished +93: ----------------------- +93: Path retrieval2 +93: Finished +93: ----------------------- +93: Unique Subgraph retrieval +93: Finished +93: ----------------------- +93: testUniqueSubgraphs2 +79: [04:03:47] ------------------------------------- +79: [04:03:47] Testing matching E/Z against Cis/Trans stereo bonds +79: [04:03:47] +79: +79: **** +79: Pre-condition Violation +79: matches must not be empty +79: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +79: Failed Expression: !matches.empty() +79: **** +79: +79: [04:03:47] +79: +79: **** +79: Pre-condition Violation +79: matches must not be empty +79: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +79: Failed Expression: !matches.empty() +79: **** +79: +79: [04:03:47] ------------------------------------- +79: [04:03:47] Test substructure matching with a pathological case for symmetric SSSR +79: [04:03:47] ------------------------------------- +79: [04:03:47] Test isAtomTerminalRGroupOrQueryHydrogen +86: [04:03:47] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +86: .[04:03:47] +86: +86: **** +86: Pre-condition Violation +86: getNumImplicitHs() called without preceding call to calcImplicitValence() +86: Violation occurred on line 291 in file ./Code/GraphMol/Atom.cpp +86: Failed Expression: d_implicitValence > -1 +86: **** +86: +86: [04:03:47] +86: +86: **** +86: Pre-condition Violation +86: getNumImplicitHs() called without preceding call to calcImplicitValence() +86: Violation occurred on line 291 in file ./Code/GraphMol/Atom.cpp +86: Failed Expression: d_implicitValence > -1 +86: **** +86: + 77/223 Test #79: testSubstructMatch ..................... Passed 0.77 sec +test 97 + Start 97: pyFilterCatalog -117: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints -117: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -117: Test timeout computed to be: 1500 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -100: processing -100: launch :0 -100: launch :1 -100: launch :2 -100: launch :3 -87: [07:34:57] == testCartesianProduct -80: Randomness seeded to: 1794068580 -80: =============================================================================== -80: All tests passed (143 assertions in 7 test cases) -80: -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" +97: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap +97: Test timeout computed to be: 1500 +86: .......[04:03:47] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +86: [04:03:47] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +86: [04:03:47] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +86: [04:03:47] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +86: .[04:03:47] product atom-mapping number 1 found multiple times. +86: [04:03:47] product atom-mapping number 1 found multiple times. +86: ................[04:03:47] mapped atoms in the reactants were not mapped in the products. +86: unmapped numbers are: 3 +86: [04:03:47] mapped atoms in the reactants were not mapped in the products. +86: unmapped numbers are: 3 +86: .[04:03:47] mapped atoms in the reactants were not mapped in the products. +86: unmapped numbers are: 3 +86: ..[04:03:47] reactant 2 has no mapped atoms. +86: [04:03:47] reactant 2 has no mapped atoms. +86: [04:03:47] product 1 has no mapped atoms. +86: ........[04:03:47] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +86: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +86: [04:03:47] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +86: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +86: .[04:03:47] reactant atom-mapping number 1 found multiple times. +86: [04:03:47] product atom-mapping number 2 not found in reactants. +86: [04:03:47] mapped atoms in the reactants were not mapped in the products. +86: unmapped numbers are: 4 +86: [04:03:47] product atom-mapping number 5 not found in reactants. +96: Warning: molecule failed filter +96: Warning: molecule failed filter: reason hzone_phenol_A(479) +96: v = { +96: 0,23}, +96: 1,22}, +96: 2,20}, +96: 3,19}, +96: 4,25}, +96: 5,24}, +96: 6,18}, +96: 7,17}, +96: 8,16}, +96: 9,21}, +96: } +96: match = { +96: 0,23}, +96: 1,22}, +96: 2,20}, +96: 3,19}, +96: 4,25}, +96: 5,24}, +96: 6,18}, +96: 7,17}, +96: 8,16}, +96: 9,21}, +96: } +96: Warning: molecule failed filter +96: Warning: molecule failed filter: reason cyano_imine_B(17) +96: v = { +96: 0,11}, +96: 1,12}, +96: 2,13}, +96: 3,14}, +96: 4,15}, +96: 5,10}, +96: 6,9}, +96: 7,8}, +96: 8,7}, +96: 9,6}, +96: 10,5}, +96: 11,17}, +96: 12,16}, +96: } +96: match = { +96: 0,11}, +96: 1,12}, +96: 2,13}, +96: 3,14}, +96: 4,15}, +96: 5,10}, +96: 6,9}, +96: 7,8}, +96: 8,7}, +96: 9,6}, +96: 10,5}, +96: 11,17}, +96: 12,16}, +96: } +96: Warning: molecule failed filter +96: Warning: molecule failed filter: reason keto_keto_gamma(5) +96: v = { +96: 0,0}, +96: 1,1}, +96: 2,2}, +96: 3,4}, +96: 4,5}, +96: 5,6}, +96: 6,7}, +96: 7,8}, +96: 8,9}, +96: 9,14}, +96: 10,15}, +96: 11,16}, +96: } +96: match = { +96: 0,0}, +96: 1,1}, +96: 2,2}, +96: 3,4}, +96: 4,5}, +96: 5,6}, +96: 6,7}, +96: 7,8}, +96: 8,9}, +96: 9,14}, +96: 10,15}, +96: 11,16}, +96: } +91: Randomness seeded to: 1296624529 +91: =============================================================================== +91: All tests passed (93 assertions in 13 test cases) +91: + 78/223 Test #91: tautomerQueryTestCatch ................. Passed 0.34 sec +test 98 + Start 98: testFragCatalog + +98: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +98: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog +98: Test timeout computed to be: 1500 +86: ........./build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> +86: png = open(fname, 'rb').read() +86: ResourceWarning: Enable tracemalloc to get the object allocation traceback +62: ..... +62: ---------------------------------------------------------------------- +62: Ran 19 tests in 0.799s +62: +62: OK +82: [04:03:47] reactant 0 has no mapped atoms. +82: [04:03:47] product 0 has no mapped atoms. +82: [04:03:47] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. +86: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 34 +86: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 36 +86: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 38 +86: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 40 +86: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 42 +86: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 87 +86: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 89 +86: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 91 +86: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 93 +86: [04:03:47] Found a SCD/SED line with missing/empty SDT specification at line 95 +81: Randomness seeded to: 1720656373 +81: =============================================================================== +81: All tests passed (9408 assertions in 38 test cases) +81: + 79/223 Test #81: testGenericGroups ...................... Passed 0.90 sec +test 99 + Start 99: pyFragCatalog + +99: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/rough_test.py" +99: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap +99: Test timeout computed to be: 1500 + 80/223 Test #82: testReaction ........................... Passed 0.90 sec +test 100 + Start 100: testDescriptors + +100: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors +100: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +100: Test timeout computed to be: 1500 +86: ..[04:03:47] SMARTS Parse Error: syntax error while parsing: boromicacid +86: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +86: [04:03:47] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +86: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +86: [04:03:47] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +86: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +86: [04:03:47] reaction has no reactants +86: [04:03:47] reaction has no products +86: [04:03:47] initialization failed +86: [04:03:47] reaction has no reactants +86: [04:03:47] reaction has no products + 81/223 Test #62: pyDepictor ............................. Passed 1.79 sec +test 101 + Start 101: testAUTOCORR2D + +101: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D +101: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +101: Test timeout computed to be: 1500 +86: .[04:03:47] SMARTS Parse Error: syntax error while parsing: boromicacid +86: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +86: [04:03:47] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +86: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +86: [04:03:47] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +86: [04:03:47] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +86: [04:03:47] reaction has no reactants +86: [04:03:47] reaction has no products +86: [04:03:47] initialization failed +86: [04:03:47] reaction has no reactants +86: [04:03:47] reaction has no products +86: . +86: ---------------------------------------------------------------------- +86: Ran 50 tests in 0.268s +86: +86: OK +86: ******************************************** +86: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +86: +98: 21 +100: [04:03:47] ------------------------------------- +100: [04:03:47] Test Crippen parameter acquisition. +100: [04:03:47] done +100: [04:03:47] ------------------------------------- +100: [04:03:47] Test Crippen calculation. 92: ..... 92: ---------------------------------------------------------------------- -92: Ran 5 tests in 0.043s +92: Ran 5 tests in 0.058s 92: 92: OK -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 76/223 Test #80: substructTestCatch ..................... Passed 0.37 sec -test 118 - Start 118: testMHFPFingerprint +87: [04:03:48] == testCartesianProduct +101: [04:03:48] ---------------------------- +101: start test autocorr2D +100: [04:03:48] done +100: [04:03:48] ------------------------------------- +100: [04:03:48] Test Issue262: problems with Crippen calculation from pickles. +100: [04:03:48] done +100: [04:03:48] ------------------------------------- +100: [04:03:48] Test AMW calculation. +100: [04:03:48] done +100: [04:03:48] ------------------------------------- +100: [04:03:48] Test Exact MW calculation. +100: [04:03:48] done +100: [04:03:48] ------------------------------------- +100: [04:03:48] Test Labute ASA descriptors. +100: [04:03:48] done +100: [04:03:48] ------------------------------------- +100: [04:03:48] Test TPSA descriptors. +87: .[04:03:48] == testEnumerateLibrary + 82/223 Test #96: filterCatalogTest ...................... Passed 0.45 sec +test 102 + Start 102: testATF -118: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint -118: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -118: Test timeout computed to be: 1500 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -88: .[07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -79: done -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -114: Randomness seeded to: 1126129511 -114: =============================================================================== -114: All tests passed (482 assertions in 7 test cases) -114: -79: [07:34:57] done -79: [07:34:57] ------------------------------------- -79: [07:34:57] Test GitHub issue 15 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -79: [07:34:57] done -79: [07:34:57] ------------------------------------- -79: [07:34:57] Test GitHub issue 409 -105: [07:34:57] done -105: [07:34:57] ------------------------------------- -105: [07:34:57] PBF edge cases. -79: [07:34:57] done -79: [07:34:57] ------------------------------------- -79: [07:34:57] Test chiral matching - 77/223 Test #114: descriptorsTestCatch ................... Passed 0.08 sec -test 119 - Start 119: testFingerprintGenerators +102: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF +102: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +102: Test timeout computed to be: 1500 +87: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> +87: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) +87: ResourceWarning: Enable tracemalloc to get the object allocation traceback + 83/223 Test #92: pyTautomerQuery ........................ Passed 0.63 sec +test 103 + Start 103: testBCUT -119: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators -119: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -119: Test timeout computed to be: 1500 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -79: [07:34:57] done -79: [07:34:57] ------------------------------------- -79: [07:34:57] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -79: [07:34:57] done -79: [07:34:57] ------------------------------------- -79: [07:34:57] Test dative-bond matching -79: [07:34:57] done -79: [07:34:57] ------------------------------------- -79: [07:34:57] Test cis/trans matching -79: [07:34:57] done -79: [07:34:57] ------------------------------------- -79: [07:34:57] Test cis/trans matching part 2 -79: [07:34:57] done -79: [07:34:57] ------------------------------------- -79: [07:34:57] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -79: [07:34:57] done -118: [07:34:57] ------------------------------------- -118: [07:34:57] Test MHFP fingerprint encoder initialization -88: .[07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. +103: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT +103: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +103: Test timeout computed to be: 1500 +88: .[04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +93: Finished +93: ----------------------- +93: testRootedSubgraphs +93: Finished +93: ----------------------- +93: testRootedPaths +93: Finished +88: .[04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. + 84/223 Test #93: testSubgraphs1 ......................... Passed 0.64 sec +test 104 + Start 104: testEEM + +104: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM +104: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +104: Test timeout computed to be: 1500 +100: [04:03:48] done +100: [04:03:48] ------------------------------------- +100: [04:03:48] Test Lipinski parameters. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. 88: () 88: ******************************************** 88: $RXN @@ -18183,13 +18128,903 @@ 88: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 88: 1 2 1 0 88: M END -88: [07:34:57] reactant 0 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] product 0 has no mapped atoms. -88: [07:34:57] Could not find RLabel mapping for atom: 0 in template: 1 -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. -88: [07:34:57] reactant 1 has no mapped atoms. +88: [04:03:48] reactant 0 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] product 0 has no mapped atoms. +88: [04:03:48] Could not find RLabel mapping for atom: 0 in template: 1 +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: [04:03:48] reactant 1 has no mapped atoms. +88: .. +88: ---------------------------------------------------------------------- +88: Ran 4 tests in 0.050s +88: +88: OK +88: +88: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +88: $RXN +88: +88: RDKit +88: +88: 2 1 +88: $MOL +88: +88: RDKit 2D +88: +88: 2 1 0 1 0 0 0 0 0 0999 V2000 +88: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 +88: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +88: 1 2 1 0 +88: M RGP 1 2 1 +88: V 1 halogen.bromine.aromatic +88: V 2 [*:1] +88: M STY 1 1 DAT +88: M SAL 1 1 1 +88: M SED 1 [#35&$([Br&$(Br-&!@c)])] +88: M END +88: $MOL +88: +88: RDKit 2D +88: +88: 4 3 0 1 0 0 0 0 0 0999 V2000 +88: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 +88: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 +88: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +88: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +88: 2 3 1 0 +88: 1 2 1 0 +88: 2 4 1 0 +88: V 2 boronicacid +88: M STY 1 1 DAT +88: M SAL 1 1 2 +88: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] +88: M END +88: $MOL +88: +88: RDKit 2D +88: +88: 2 1 0 0 0 0 0 0 0 0999 V2000 +88: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 +88: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 +88: 1 2 1 0 +88: M RGP 1 1 1 +88: V 1 [*:1] +88: M END +88: +88: $RXN Failed +103: [04:03:48] ------------------------------------- +103: [04:03:48] Basic BCUT tests. + 85/223 Test #102: testATF ................................ Passed 0.11 sec +test 105 + Start 105: testPBF + +105: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF +105: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +105: Test timeout computed to be: 1500 +87: ..[04:03:48] == testRGroupState +103: [04:03:48] done +103: [04:03:48] ------------------------------------- +103: [04:03:48] Larger BCUT tests. +104: =>start test EEM +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: 0 +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 86/223 Test #86: pyChemReactions ........................ Passed 1.09 sec +test 106 + Start 106: testRDFcustom + +106: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom +106: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +106: Test timeout computed to be: 1500 +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +87: .[04:03:48] == testRandomEnumerateAllBBsLibrary +87: ** [1, 1] +87: ** [0, 2] +87: ** [1, 0] +105: [04:03:48] ------------------------------------- +105: [04:03:48] Basic PBF tests. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +87: .[04:03:48] == testRandomEnumerateLibrary +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +87: .[04:03:48] == testRandomSample +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +87: .[04:03:48] == testRandomSampleAllBBs +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +87: .[04:03:48] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +87: [04:03:48] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +87: .[04:03:48] == testRemoveBadMatches +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +87: .[04:03:48] == testTimings +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 87/223 Test #88: pyChemReactionSanitize ................. Passed 1.22 sec +test 107 + Start 107: testRDF + +107: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF +107: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +107: Test timeout computed to be: 1500 +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +105: [04:03:48] done +105: [04:03:48] ------------------------------------- +105: [04:03:48] PBF edge cases. +105: [04:03:48] done +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: 100 +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 88/223 Test #105: testPBF ................................ Passed 0.32 sec +test 108 + Start 108: testMORSE + +108: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE +108: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +108: Test timeout computed to be: 1500 +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +100: [04:03:48] done +100: [04:03:48] ------------------------------------- +100: [04:03:48] Test VSA descriptors. +100: [04:03:48] done +100: [04:03:48] ------------------------------------- +100: [04:03:48] Test molecular formula calculation. +100: [04:03:48] done +100: [04:03:48] ------------------------------------- +100: [04:03:48] Test Issue 3415534. +100: [04:03:48] done +100: [04:03:48] ------------------------------------- +100: [04:03:48] Test Issue3433771: Bad definition for Crippen atom type O11. +100: [04:03:48] done +100: [04:03:48] ------------------------------------- +100: [04:03:48] Test multithreading +100: reading molecules +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +100: processing +100: launch :0 +100: launch :1 +100: launch :2 +100: launch :3 +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: [04:03:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +64: [04:03:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +64: [04:03:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +64: [04:03:48] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: [04:03:48] deprecated group abbreviation ignored on line 24 +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +64: [04:03:48] +64: +64: **** +64: Post-condition Violation +64: Element 'Mv' not found +64: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +64: Failed Expression: anum > -1 +64: **** +64: +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: 200 +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +101: [04:03:48] done +101: [04:03:48] ------------------------------------- +101: [04:03:48] Test Github #3806: NaNs from AUTOCORR2D descriptor +101: [04:03:48] done +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 89/223 Test #101: testAUTOCORR2D ......................... Passed 0.99 sec +test 109 + Start 109: test3D + +109: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D +109: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +109: Test timeout computed to be: 1500 +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +99: ......... +99: ---------------------------------------------------------------------- +99: Ran 9 tests in 0.183s +99: +99: OK +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +109: [04:03:49] ------------------------------------- +109: [04:03:49] Basic PMI tests. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: 300 +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [04:03:49] ------------------------------------- +103: [04:03:49] Test empty molecule BCUT. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 90/223 Test #103: testBCUT ............................... Passed 1.11 sec +test 110 + Start 110: testWHIM + +110: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM +110: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +110: Test timeout computed to be: 1500 +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 91/223 Test #99: pyFragCatalog .......................... Passed 1.36 sec +test 111 + Start 111: testGETAWAY + +111: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY +111: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +111: Test timeout computed to be: 1500 +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: 400 +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [04:03:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: Elapsed time: 1.25173 s +104: Errors:0 +104: [04:03:49] test on : 500 molecules done + 92/223 Test #104: testEEM ................................ Passed 1.31 sec +test 112 + Start 112: testAUTOCORR3D + +112: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D +112: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +112: Test timeout computed to be: 1500 +106: =>start test rdf custom +106: [04:03:49] test on : 365 molecules done +97: .............[04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +97: [04:03:49] SMILES Parse Error: syntax error while parsing: --- +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +97: [04:03:49] dasfsadf +98: [04:03:49] +98: +98: **** +98: Invariant Violation +98: nonsense +98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +98: Failed Expression: token != tokens.end() +98: **** +98: +98: [04:03:49] +98: +98: **** +98: Invariant Violation +98: nonsense no new line +98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +98: Failed Expression: token != tokens.end() +98: **** +98: +98: [04:03:49] +98: +98: **** +98: Invariant Violation +98: nonsense with tab +98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +98: Failed Expression: token != tokens.end() +98: **** +98: + 93/223 Test #98: testFragCatalog ........................ Passed 1.77 sec +test 113 + Start 113: testCoulombMat + +113: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat +113: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +113: Test timeout computed to be: 1500 +113: ===================== Testing CoulombMat ======================= +109: [04:03:49] done +109: [04:03:49] ------------------------------------- +109: [04:03:49] More PMI/NPR tests. +109: [04:03:49] done +109: [04:03:49] ------------------------------------- +109: [04:03:49] Basic NPR tests. +113: CM test 1 mat Done + 94/223 Test #113: testCoulombMat ......................... Passed 0.07 sec +test 114 + Start 114: descriptorsTestCatch + +114: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch +114: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +114: Test timeout computed to be: 1500 +110: =>start test WHIM +110: [04:03:49] test on : 365 molecules done + 95/223 Test #110: testWHIM ............................... Passed 0.53 sec +test 115 + Start 115: pyMolDescriptors + +115: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" +115: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap +115: Test timeout computed to be: 1500 +97: .[04:03:49] SMILES Parse Error: syntax error while parsing: mydoghasfleas +97: [04:03:49] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +114: Randomness seeded to: 3292093798 +114: =============================================================================== +114: All tests passed (482 assertions in 7 test cases) +114: + 96/223 Test #114: descriptorsTestCatch ................... Passed 0.17 sec +test 116 + Start 116: pyMolDescriptors3D + +116: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/test3D.py" +116: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap +116: Test timeout computed to be: 1500 +97: ....... +97: ---------------------------------------------------------------------- +97: Ran 21 tests in 1.720s +97: +97: OK +97: (Five aromatic carbons And (Not any of Five aromatic carbons)) +97: (Five aromatic carbons Or (Not any of Five aromatic carbons)) +97: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) +97: ******************************************** +97: Testing: PAINS_A 2 +97: ******************************************** +97: Testing: PAINS_B 4 +97: ******************************************** +97: Testing: PAINS_C 8 +97: ******************************************** +97: Testing: PAINS 14 +97: (Not FilterMatcher) +97: Bar +97: Count 1 +97: ******************************************** +97: {'Cl,Br,I'} +97: 1 +97: 2 +97: running +112: =>start test autocorr3D +112: [04:03:50] test on : 365 molecules done + 97/223 Test #112: testAUTOCORR3D ......................... Passed 0.77 sec +test 117 + Start 117: testFingerprints + +117: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints +117: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +117: Test timeout computed to be: 1500 117: 117: 117: @@ -18253,73 +19088,6 @@ 117: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 4 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 5 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 -105: [07:34:57] done -87: .[07:34:57] == testEnumerateLibrary -88: .. -88: ---------------------------------------------------------------------- -88: Ran 4 tests in 0.025s -88: -88: OK -88: -88: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -88: $RXN -88: -88: RDKit -88: -88: 2 1 -88: $MOL -88: -88: RDKit 2D -88: -88: 2 1 0 1 0 0 0 0 0 0999 V2000 -88: -3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -88: -3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -88: 1 2 1 0 -88: M RGP 1 2 1 -88: V 1 halogen.bromine.aromatic -88: V 2 [*:1] -88: M STY 1 1 DAT -88: M SAL 1 1 1 -88: M SED 1 [#35&$([Br&$(Br-&!@c)])] -88: M END -88: $MOL -88: -88: RDKit 2D -88: -88: 4 3 0 1 0 0 0 0 0 0999 V2000 -88: 3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0 -88: 4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0 -88: 4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -88: 4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -88: 2 3 1 0 -88: 1 2 1 0 -88: 2 4 1 0 -88: V 2 boronicacid -88: M STY 1 1 DAT -88: M SAL 1 1 2 -88: M SED 1 [#5&$([$(B-&!@[#6])](O)O)] -88: M END -88: $MOL -88: -88: RDKit 2D -88: -88: 2 1 0 0 0 0 0 0 0 0999 V2000 -88: 11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0 -88: 11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0 -88: 1 2 1 0 -88: M RGP 1 1 1 -88: V 1 [*:1] -88: M END -88: -88: $RXN Failed -86: [07:34:57] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead - 78/223 Test #105: testPBF ................................ Passed 0.28 sec -test 120 - Start 120: fpTestCatch - -120: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch -120: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -120: Test timeout computed to be: 1500 117: 6 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 7 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 @@ -18470,15 +19238,6 @@ 117: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 6 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 7 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 -79: [07:34:57] ------------------------------------- -79: [07:34:57] Testing matching E/Z against Cis/Trans stereo bonds -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: 200 -104: [07:34:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -87: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> -87: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) -87: ResourceWarning: Enable tracemalloc to get the object allocation traceback 117: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 9 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 10 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 @@ -18545,8 +19304,6 @@ 117: 117: SMI: n1c[nH]c2cc(O)nc(O)c21 117: Atoms: -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 117: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 @@ -18565,15 +19322,6 @@ 117: 3 3->4 order: 12 conj?: 1 aromatic?: 1 117: 4 4->5 order: 12 conj?: 1 aromatic?: 1 117: 5 5->6 order: 1 conj?: 1 aromatic?: 0 -79: [07:34:58] -79: -79: **** -79: Pre-condition Violation -79: matches must not be empty -79: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -79: Failed Expression: !matches.empty() -79: **** -79: 117: 6 5->7 order: 12 conj?: 1 aromatic?: 1 117: 7 7->8 order: 12 conj?: 1 aromatic?: 1 117: 8 8->9 order: 1 conj?: 1 aromatic?: 0 @@ -18671,40 +19419,7 @@ 117: 1 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 2 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 -79: [07:34:58] -79: -79: **** -79: Pre-condition Violation -79: matches must not be empty -79: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -79: Failed Expression: !matches.empty() -79: **** -79: -79: [07:34:58] ------------------------------------- -79: [07:34:58] Test substructure matching with a pathological case for symmetric SSSR -79: [07:34:58] ------------------------------------- -79: [07:34:58] Test isAtomTerminalRGroupOrQueryHydrogen -86: [07:34:58] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -86: .[07:34:58] -86: -86: **** -86: Pre-condition Violation -86: getNumImplicitHs() called without preceding call to calcImplicitValence() -86: Violation occurred on line 291 in file ./Code/GraphMol/Atom.cpp -86: Failed Expression: d_implicitValence > -1 -86: **** -86: -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: 4 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 -86: [07:34:58] -86: -86: **** -86: Pre-condition Violation -86: getNumImplicitHs() called without preceding call to calcImplicitValence() -86: Violation occurred on line 291 in file ./Code/GraphMol/Atom.cpp -86: Failed Expression: d_implicitValence > -1 -86: **** -86: 117: 5 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 117: 6 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 3 arom?: 0 chi: 0 117: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 @@ -18717,8 +19432,6 @@ 117: 2 2->3 order: 12 conj?: 1 aromatic?: 1 117: 3 3->4 order: 12 conj?: 1 aromatic?: 1 117: 4 4->5 order: 12 conj?: 1 aromatic?: 1 -33: [07:34:58] Maximum BFS search size exceeded. -33: This is likely due to a highly symmetric fused ring system. 117: 5 5->6 order: 1 conj?: 1 aromatic?: 0 117: 6 5->7 order: 12 conj?: 1 aromatic?: 1 117: 7 3->8 order: 12 conj?: 1 aromatic?: 1 @@ -18736,8 +19449,6 @@ 117: 117: 117: ------------------- -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test atom-pair fp generator 117: 117: SMI: n1c(O)cc2[nH]cnc2c1O 117: Atoms: @@ -18786,7 +19497,6 @@ 117: 117: 117: ------------------- -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: 117: 117: @@ -18798,346 +19508,288 @@ 117: 117: ------------------- 117: - 79/223 Test #79: testSubstructMatch ..................... Passed 0.45 sec +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Morgan Fingerprints. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Morgan Fingerprints using fromAtoms argument. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Morgan Fingerprints as bit vects. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Morgan Fingerprints with feature invariants. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test additional Morgan fingerprints options. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Atom Codes. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Atom Pairs. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Atom Pairs part 2. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Topological Torsions. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Bulk Topological Torsions. +109: [04:03:50] done +109: [04:03:50] ------------------------------------- +109: [04:03:50] PMI edge cases. +109: [04:03:50] done +109: [04:03:50] ------------------------------------- +109: [04:03:50] NPR edge cases. +109: [04:03:50] done +109: [04:03:50] ------------------------------------- +109: [04:03:50] 3D descriptors. +109: [04:03:50] done +109: [04:03:50] ------------------------------------- +109: [04:03:50] 3D descriptor edge cases. +109: [04:03:50] done +109: [04:03:50] ------------------------------------- +109: [04:03:50] Inertial shape factor. +109: [04:03:50] done + 98/223 Test #97: pyFilterCatalog ........................ Passed 2.84 sec + 99/223 Test #109: test3D ................................. Passed 1.63 sec +test 118 + Start 118: testMHFPFingerprint + +118: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint +118: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +118: Test timeout computed to be: 1500 +test 119 + Start 119: testFingerprintGenerators + +119: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators +119: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +119: Test timeout computed to be: 1500 +118: [04:03:50] ------------------------------------- +118: [04:03:50] Test MHFP fingerprint encoder initialization +118: [04:03:50] done +118: [04:03:50] ------------------------------------- +118: [04:03:50] Test MHFP shingling creation +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test atom-pair fp generator +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Hashed Atom Pairs. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Hashed torsions. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Rooted Atom Pairs. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test ignoring atoms in Atom Pairs. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Rooted Topological Torsions. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test ignoring atoms in Topological Torsions. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test atom info from morgan fingerprints. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test atom info from morgan fingerprints including Info Redundant Environments. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] ------------------------------------- +117: [04:03:50] ------------------------------------- +117: [04:03:50] ------------------------------------- +117: [04:03:50] ------------------------------------- +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Atom Pairs including info about chirality. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test Topological Torsions including info about chirality. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test GitHub Issue 25: fingerprint backwards compatibility. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test GitHub Issue 151: PatternFingerprint problems +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test atom-pair fp generator with different arguments +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +118: [04:03:50] done +118: [04:03:50] ------------------------------------- +118: [04:03:50] Test MHFP hashing of string and uint arrays +118: [04:03:50] done +118: [04:03:50] ------------------------------------- +118: [04:03:50] Test SECFP fingerprint functionality +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test 3D atom pairs. +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +117: [04:03:50] done +117: [04:03:50] ------------------------------------- +117: [04:03:50] Test multithreading with the pattern FP +117: reading molecules +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test atom-pair additional output +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test Folded Atom Pairs. +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test Rooted Atom Pairs. +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test ignoring atoms in Atom Pairs. +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test Atom Pairs including info about chirality. +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test Morgan Fingerprints. +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test morgan fp generator +87: . +87: ---------------------------------------------------------------------- +87: Ran 11 tests in 2.831s +87: +87: OK +87: True +87: == CartesianProductStrategy CartesianProductStrategy +87: 197 out of 300 +87: 0 6 out of 10 +87: 1 3 out of 5 +87: 2 4 out of 6 +87: 198 out of 300 +87: 0 10 out of 10 +87: 1 5 out of 5 +87: 2 6 out of 6 +87: Skipped 10000000 in 0.08026814460754395 seconds +87: Skipped 10000000 in 1.4736523628234863 seconds +87: Skipped 10000000 in 0.60964035987854 seconds +118: [04:03:50] done +100/223 Test #118: testMHFPFingerprint .................... Passed 0.28 sec +test 120 + Start 120: fpTestCatch + +120: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch +120: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +120: Test timeout computed to be: 1500 +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test Morgan Fingerprints using fromAtoms argument. +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test Morgan Fingerprints as bit vects. +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test Morgan Fingerprints with feature invariants. +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test additional Morgan fingerprints options. +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Single atoms setting radius 1 bits in Morgan fingerprints +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test different invariant generator combinations +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test invariant overriding +119: [04:03:50] done +119: [04:03:50] ------------------------------------- +119: [04:03:50] Test RDKit fp generator +120: Randomness seeded to: 2297225846 +120: =============================================================================== +120: All tests passed (166 assertions in 14 test cases) +120: +101/223 Test #120: fpTestCatch ............................ Passed 0.06 sec test 121 Start 121: fpGenTestCatch 121: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 121: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints 121: Test timeout computed to be: 1500 -118: [07:34:58] done -118: [07:34:58] ------------------------------------- -118: [07:34:58] Test MHFP shingling creation -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 80/223 Test #92: pyTautomerQuery ........................ Passed 0.38 sec +117: pass 1 +117: launch :0 +117: launch :1 +117: launch :2 +117: launch :3 +121: Randomness seeded to: 2573219790 +121: =============================================================================== +121: All tests passed (2678 assertions in 4 test cases) +121: +102/223 Test #121: fpGenTestCatch ......................... Passed 0.38 sec test 122 Start 122: pyTestGenerator 122: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 122: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 122: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -86: .......[07:34:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -86: [07:34:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -86: [07:34:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -86: [07:34:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -86: .[07:34:58] product atom-mapping number 1 found multiple times. -86: [07:34:58] product atom-mapping number 1 found multiple times. -27: ......[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -27: [07:34:58] -27: -27: **** -27: Invariant Violation -27: bad direction in linearSearch -27: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h -27: Failed Expression: status >= 0 -27: **** -27: -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test atom-pair fp generator with different arguments -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -109: [07:34:58] done -109: [07:34:58] ------------------------------------- -109: [07:34:58] More PMI/NPR tests. -109: [07:34:58] done -109: [07:34:58] ------------------------------------- -109: [07:34:58] Basic NPR tests. -82: [07:34:58] reactant 0 has no mapped atoms. -82: [07:34:58] product 0 has no mapped atoms. -82: [07:34:58] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. -81: Randomness seeded to: 3379151290 -81: =============================================================================== -81: All tests passed (9408 assertions in 38 test cases) -81: -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Morgan Fingerprints. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Morgan Fingerprints using fromAtoms argument. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Morgan Fingerprints as bit vects. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Morgan Fingerprints with feature invariants. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test additional Morgan fingerprints options. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Atom Codes. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Atom Pairs. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Atom Pairs part 2. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Topological Torsions. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Bulk Topological Torsions. - 81/223 Test #81: testGenericGroups ...................... Passed 0.43 sec +103/223 Test #87: pyChemReactionEnumerations ............. Passed 4.16 sec test 123 Start 123: pyTestMHFP 123: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 123: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 123: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -86: ................[07:34:58] mapped atoms in the reactants were not mapped in the products. -86: unmapped numbers are: 3 -86: [07:34:58] mapped atoms in the reactants were not mapped in the products. -86: unmapped numbers are: 3 -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test atom-pair additional output -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test Folded Atom Pairs. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test Rooted Atom Pairs. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test ignoring atoms in Atom Pairs. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test Atom Pairs including info about chirality. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test Morgan Fingerprints. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test morgan fp generator -99: ......... -99: ---------------------------------------------------------------------- -99: Ran 9 tests in 0.063s -99: -99: OK - 82/223 Test #82: testReaction ........................... Passed 0.43 sec +106: =>start test morse custom +106: [04:03:51] test on : 365 molecules done +117: pass 2 +117: launch :0 +117: launch :1 +117: launch :2 +117: launch :3 +116: ........ +116: ---------------------------------------------------------------------- +116: Ran 8 tests in 0.657s +116: +116: OK +108: =>start test MORSE +108: =>read file +108: [04:03:51] test on : 365 molecules done +107: =>start test rdf +107: [04:03:51] test on : 365 molecules done +104/223 Test #108: testMORSE .............................. Passed 3.45 sec test 124 Start 124: testPartialCharges 124: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 124: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges 124: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -86: .[07:34:58] mapped atoms in the reactants were not mapped in the products. -86: unmapped numbers are: 3 -118: [07:34:58] done -118: [07:34:58] ------------------------------------- -118: [07:34:58] Test MHFP hashing of string and uint arrays -118: [07:34:58] done -118: [07:34:58] ------------------------------------- -118: [07:34:58] Test SECFP fingerprint functionality -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -86: ..[07:34:58] reactant 2 has no mapped atoms. -86: [07:34:58] reactant 2 has no mapped atoms. -86: [07:34:58] product 1 has no mapped atoms. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -87: ..[07:34:58] == testRGroupState -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test Morgan Fingerprints using fromAtoms argument. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test Morgan Fingerprints as bit vects. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test Morgan Fingerprints with feature invariants. -118: [07:34:58] done -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test additional Morgan fingerprints options. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints - 83/223 Test #118: testMHFPFingerprint .................... Passed 0.08 sec +105/223 Test #107: testRDF ................................ Passed 3.60 sec test 125 Start 125: pyPartialCharges 125: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 125: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 125: Test timeout computed to be: 1500 -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Single atoms setting radius 1 bits in Morgan fingerprints -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test different invariant generator combinations -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test invariant overriding -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test RDKit fp generator -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -87: .[07:34:58] == testRandomEnumerateAllBBsLibrary -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -86: ........[07:34:58] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -86: [07:34:58] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -87: ** [1, 1] -87: ** [0, 2] -87: ** [1, 0] -86: .[07:34:58] reactant atom-mapping number 1 found multiple times. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -86: [07:34:58] product atom-mapping number 2 not found in reactants. -120: Randomness seeded to: 1986149471 -120: =============================================================================== -120: All tests passed (166 assertions in 14 test cases) -120: -86: [07:34:58] mapped atoms in the reactants were not mapped in the products. -86: unmapped numbers are: 4 -86: [07:34:58] product atom-mapping number 5 not found in reactants. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 84/223 Test #120: fpTestCatch ............................ Passed 0.07 sec - 85/223 Test #124: testPartialCharges ..................... Passed 0.03 sec +106/223 Test #124: testPartialCharges ..................... Passed 0.08 sec test 126 Start 126: testMolTransforms 126: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 126: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms 126: Test timeout computed to be: 1500 +107/223 Test #116: pyMolDescriptors3D ..................... Passed 2.28 sec test 127 Start 127: pyMolTransforms 127: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 127: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap 127: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -87: .[07:34:58] == testRandomEnumerateLibrary - 86/223 Test #88: pyChemReactionSanitize ................. Passed 0.45 sec -test 128 - Start 128: testMMFFForceFieldHelpers - -128: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers -128: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF -128: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -87: .[07:34:58] == testRandomSample -62: ..............[07:34:58] SMILES Parse Error: syntax error while parsing: invalidsmiles -62: [07:34:58] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -87: .[07:34:58] == testRandomSampleAllBBs -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -101: [07:34:58] done - 87/223 Test #99: pyFragCatalog .......................... Passed 0.43 sec -test 129 - Start 129: testMMFFForceFieldHelpersMultiThread - -129: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread -129: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF -129: Test timeout computed to be: 1500 -101: [07:34:58] ------------------------------------- -101: [07:34:58] Test Github #3806: NaNs from AUTOCORR2D descriptor -101: [07:34:58] done -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [07:34:58] ------------------------------------- -128: [07:34:58] Test MMFF atom types. - 88/223 Test #101: testAUTOCORR2D ......................... Passed 0.42 sec -test 130 - Start 130: testUFFForceFieldHelpers - -130: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers -130: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF -130: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -86: ........./build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> -86: png = open(fname, 'rb').read() -86: ResourceWarning: Enable tracemalloc to get the object allocation traceback -86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 34 -86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 36 -86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 38 -86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 40 -86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 42 -87: .[07:34:58] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -87: [07:34:58] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -87: .[07:34:58] == testRemoveBadMatches -87: .[07:34:58] == testTimings -86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 87 -86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 89 -86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 91 -86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 93 -86: [07:34:58] Found a SCD/SED line with missing/empty SDT specification at line 95 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [07:34:58] done -128: [07:34:58] ------------------------------------- -128: [07:34:58] Testing MMFF builder tools. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 126: *********************************************************** 126: Testing MolTransforms 126: --------------------------------- @@ -19168,166 +19820,71 @@ 126: testWeightedCentroid 126: 126: *********************************************************** -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 89/223 Test #126: testMolTransforms ...................... Passed 0.06 sec -test 131 - Start 131: testCrystalForceField +108/223 Test #126: testMolTransforms ...................... Passed 0.25 sec +test 128 + Start 128: testMMFFForceFieldHelpers -131: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField -131: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF -131: Test timeout computed to be: 1500 -86: ..[07:34:58] SMARTS Parse Error: syntax error while parsing: boromicacid -86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [07:34:58] ------------------------------------- -130: [07:34:58] Test UFF atom labels. -129: [07:34:58] ------------------------------------- -129: [07:34:58] Test MMFF multithreading -86: [07:34:58] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -86: [07:34:58] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -86: [07:34:58] reaction has no reactants -86: [07:34:58] reaction has no products -86: [07:34:58] initialization failed -86: [07:34:58] reaction has no reactants -86: [07:34:58] reaction has no products -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [07:34:58] done -128: [07:34:58] ------------------------------------- -128: [07:34:58] Testing MMFF builder+minimization. -104: 300 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: ------------------------------------- -131: Test CrystalFF torsional term. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [07:34:58] done -130: [07:34:58] ------------------------------------- -130: [07:34:58] Test UFF atom typer. -86: .[07:34:58] SMARTS Parse Error: syntax error while parsing: boromicacid -86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -86: [07:34:58] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -86: [07:34:58] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -86: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -86: [07:34:58] reaction has no reactants -86: [07:34:58] reaction has no products -86: [07:34:58] initialization failed -86: [07:34:58] reaction has no reactants -86: [07:34:58] reaction has no products -86: . -86: ---------------------------------------------------------------------- -86: Ran 50 tests in 0.157s -86: -86: OK -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -86: ******************************************** -86: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -86: -130: [07:34:58] done -130: [07:34:58] ------------------------------------- -130: [07:34:58] Testing UFF builder tools. -130: [07:34:58] done -130: [07:34:58] ------------------------------------- -130: [07:34:58] Testing UFF builder+minimization. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -110: =>start test WHIM -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -110: [07:34:58] test on : 365 molecules done -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 90/223 Test #110: testWHIM ............................... Passed 0.40 sec -test 132 - Start 132: pyForceFieldHelpers +128: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers +128: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF +128: Test timeout computed to be: 1500 +128: [04:03:52] ------------------------------------- +128: [04:03:52] Test MMFF atom types. +119: [04:03:52] done +119: [04:03:52] ------------------------------------- +119: [04:03:52] Test unfolded version of RDKFP +119: [04:03:52] ------------------------------------- +119: [04:03:52] Test topological torsion fp generator +128: [04:03:52] done +128: [04:03:52] ------------------------------------- +128: [04:03:52] Testing MMFF builder tools. +128: [04:03:52] done +128: [04:03:52] ------------------------------------- +128: [04:03:52] Testing MMFF builder+minimization. +119: [04:03:52] done +119: [04:03:52] ------------------------------------- +119: [04:03:52] Test Topological Torsions. +119: [04:03:52] done +119: [04:03:52] ------------------------------------- +119: [04:03:52] Test Folded torsions. +119: [04:03:52] done +119: [04:03:52] ------------------------------------- +119: [04:03:52] Test Bulk Topological Torsions. +122: ............. +122: ---------------------------------------------------------------------- +122: Ran 13 tests in 0.431s +122: +122: OK +123: .. +123: ---------------------------------------------------------------------- +123: Ran 2 tests in 0.137s +123: +123: OK +109/223 Test #38: hanoiTest .............................. Passed 7.17 sec +test 129 + Start 129: testMMFFForceFieldHelpersMultiThread -132: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" -132: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap -132: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -4: dynamic RDAny:0.37222 s -4: static RDValue:1e-06 s -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [07:34:58] done -128: [07:34:58] ------------------------------------- -128: [07:34:58] Testing Issue239. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Hashed Atom Pairs. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Hashed torsions. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Rooted Atom Pairs. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test ignoring atoms in Atom Pairs. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Rooted Topological Torsions. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test ignoring atoms in Topological Torsions. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test atom info from morgan fingerprints. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -117: [07:34:58] Test atom info from morgan fingerprints including Info Redundant Environments. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] ------------------------------------- +129: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread +129: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF +129: Test timeout computed to be: 1500 +128: [04:03:52] done +128: [04:03:52] ------------------------------------- +128: [04:03:52] Testing Issue239. +129: [04:03:52] ------------------------------------- +129: [04:03:52] Test MMFF multithreading +115: .....[04:03:52] +115: +115: **** +115: Pre-condition Violation +115: Number of atom props not equal to number of atoms +115: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp +115: Failed Expression: atom_props.size() == num_atoms +115: **** +115: +128: [04:03:52] done +128: [04:03:52] ------------------------------------- +128: [04:03:52] Testing calcEnergy with passed coords. 129: processing 129: launch :0 -117: [07:34:58] ------------------------------------- 129: launch :1 129: launch :2 129: launch :3 @@ -19348,373 +19905,508 @@ 129: launch :18 129: launch :19 129: launch :20 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 129: launch :21 129: launch :22 129: launch :23 -62: ..... -62: ---------------------------------------------------------------------- -62: Ran 19 tests in 0.421s -62: -62: OK -121: Randomness seeded to: 755712616 -121: =============================================================================== -121: All tests passed (2678 assertions in 4 test cases) -121: -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -117: [07:34:58] ------------------------------------- -117: [07:34:58] ------------------------------------- -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Atom Pairs including info about chirality. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test Topological Torsions including info about chirality. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test GitHub Issue 25: fingerprint backwards compatibility. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test GitHub Issue 151: PatternFingerprint problems - 91/223 Test #121: fpGenTestCatch ......................... Passed 0.21 sec +115: ......................... +115: ---------------------------------------------------------------------- +115: Ran 30 tests in 0.165s +115: +115: OK +115: exactmw 78.046950192 +115: amw 78.11399999999999 +115: lipinskiHBA 0.0 +115: lipinskiHBD 0.0 +115: NumRotatableBonds 0.0 +115: NumHBD 0.0 +115: NumHBA 0.0 +115: NumHeavyAtoms 6.0 +115: NumAtoms 6.0 +115: NumHeteroatoms 0.0 +115: NumAmideBonds 0.0 +115: FractionCSP3 0.0 +115: NumRings 1.0 +115: NumAromaticRings 1.0 +115: NumAliphaticRings 0.0 +115: NumSaturatedRings 0.0 +115: NumHeterocycles 0.0 +115: NumAromaticHeterocycles 0.0 +115: NumSaturatedHeterocycles 0.0 +115: NumAliphaticHeterocycles 0.0 +115: NumSpiroAtoms 0.0 +115: NumBridgeheadAtoms 0.0 +115: NumAtomStereoCenters 0.0 +115: NumUnspecifiedAtomStereoCenters 0.0 +115: labuteASA 37.43140311949697 +115: tpsa 0.0 +115: CrippenClogP 1.6866 +115: CrippenMR 26.441999999999993 +115: chi0v 3.464101615137755 +115: chi1v 2.0000000000000004 +115: chi2v 0.6666666666666671 +115: chi3v 0.6666666666666671 +115: chi4v 0.38490017945975075 +115: chi0n 3.464101615137755 +115: chi1n 2.0000000000000004 +115: chi2n 0.6666666666666671 +115: chi3n 0.6666666666666671 +115: chi4n 0.38490017945975075 +115: hallKierAlpha -0.78 +115: kappa1 3.4115708812260532 +115: kappa2 1.6057694396735218 +115: kappa3 0.5823992601400448 +115: Phi 0.9130327103921437 +115: exactmw 78.046950192 +115: lipinskiHBA 0.0 +110/223 Test #122: pyTestGenerator ........................ Passed 1.78 sec +test 130 + Start 130: testUFFForceFieldHelpers + +130: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers +130: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF +130: Test timeout computed to be: 1500 +128: [04:03:53] done +128: [04:03:53] ------------------------------------- +128: [04:03:53] Testing calcGrad. +111/223 Test #123: pyTestMHFP ............................. Passed 1.79 sec +test 131 + Start 131: testCrystalForceField + +131: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField +131: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF +131: Test timeout computed to be: 1500 +130: [04:03:53] ------------------------------------- +130: [04:03:53] Test UFF atom labels. +131: ------------------------------------- +131: Test CrystalFF torsional term. +127: ........ +127: ---------------------------------------------------------------------- +127: Ran 8 tests in 0.108s +127: +127: OK +119: [04:03:53] done +119: [04:03:53] ------------------------------------- +119: [04:03:53] Test Rooted Topological Torsions. +119: [04:03:53] done +119: [04:03:53] ------------------------------------- +119: [04:03:53] Test ignoring atoms in Topological Torsions. +119: [04:03:53] done +119: [04:03:53] ------------------------------------- +130: [04:03:53] done +130: [04:03:53] ------------------------------------- +130: [04:03:53] Test UFF atom typer. +130: [04:03:53] done +130: [04:03:53] ------------------------------------- +130: [04:03:53] Testing UFF builder tools. +130: [04:03:53] done +130: [04:03:53] ------------------------------------- +130: [04:03:53] Testing UFF builder+minimization. +119: [04:03:53] ------------------------------------- +119: [04:03:53] Test Topological Torsions including info about chirality. +119: [04:03:53] done +119: [04:03:53] ------------------------------------- +119: [04:03:53] Test GitHub Issue 25: fingerprint backwards compatibility. +119: [04:03:53] done +119: [04:03:53] ------------------------------------- +119: [04:03:53] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +119: [04:03:53] done +119: [04:03:53] ------------------------------------- +119: [04:03:53] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +119: [04:03:53] done +119: [04:03:53] ------------------------------------- +119: [04:03:53] Test convenience and bulk fp calculation functions +106: =>start test AUTOCORR3D custom +106: [04:03:53] test on : 365 molecules done +128: [04:03:53] done +128: [04:03:53] ------------------------------------- +128: [04:03:53] Testing Issue242. +112/223 Test #127: pyMolTransforms ........................ Passed 1.22 sec +test 132 + Start 132: pyForceFieldHelpers + +132: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" +132: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap +132: Test timeout computed to be: 1500 +128: [04:03:53] done +128: [04:03:53] ------------------------------------- +128: [04:03:53] Testing github 308: crash during MMFF parameterization . +128: [04:03:53] ------------------------------------- +128: [04:03:53] Testing SFIssue1653802. +128: [04:03:53] done +128: [04:03:53] ------------------------------------- +128: [04:03:53] Testing SFIssue2378119. +128: [04:03:53] done +128: [04:03:53] ------------------------------------- +128: [04:03:53] Test MMFF force-field parameter getters. +128: [04:03:53] ------------------------------------- +128: [04:03:53] Test MMFF multithreading +128: generating reference data +113/223 Test #115: pyMolDescriptors ....................... Passed 3.75 sec test 133 Start 133: testDistGeomHelpers 133: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 133: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers 133: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [07:34:58] done -128: [07:34:58] ------------------------------------- -128: [07:34:58] Testing calcEnergy with passed coords. - 92/223 Test #86: pyChemReactions ........................ Passed 0.61 sec +130: [04:03:53] done +130: [04:03:53] ------------------------------------- +130: [04:03:53] Testing UFF special cases. +130: [04:03:53] UFFTYPER: Unrecognized charge state for atom: 0 +130: [04:03:53] done +130: [04:03:53] ------------------------------------- +130: [04:03:53] Testing Issue239. +133: go +133: ------------------------------------- +133: +129: done +130: [04:03:53] done +130: [04:03:53] ------------------------------------- +130: [04:03:53] Testing calcEnergy with passed coords. +129: [04:03:53] done +114/223 Test #131: testCrystalForceField .................. Passed 0.57 sec test 134 Start 134: distGeomHelpersCatch 134: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 134: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers 134: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test 3D atom pairs. -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -117: [07:34:58] done -117: [07:34:58] ------------------------------------- -117: [07:34:58] Test multithreading with the pattern FP -117: reading molecules -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [07:34:58] done -128: [07:34:58] ------------------------------------- -128: [07:34:58] Testing calcGrad. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -109: [07:34:58] done -109: [07:34:58] ------------------------------------- -109: [07:34:58] PMI edge cases. -109: [07:34:58] done -109: [07:34:58] ------------------------------------- -109: [07:34:58] NPR edge cases. -109: [07:34:58] done -109: [07:34:58] ------------------------------------- -109: [07:34:58] 3D descriptors. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -109: [07:34:58] done -109: [07:34:58] ------------------------------------- -109: [07:34:58] 3D descriptor edge cases. -109: [07:34:58] done -109: [07:34:58] ------------------------------------- -109: [07:34:58] Inertial shape factor. -109: [07:34:58] done -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 93/223 Test #109: test3D ................................. Passed 0.51 sec +130: [04:03:53] done +130: [04:03:53] ------------------------------------- +130: [04:03:53] Testing calcGrad. +130: [04:03:53] done +130: [04:03:53] ------------------------------------- +130: [04:03:53] Testing SFIssue1653802. +130: [04:03:53] done +130: [04:03:53] ------------------------------------- +130: [04:03:53] Testing SFIssue2378119. +130: [04:03:53] done +130: [04:03:53] ------------------------------------- +130: [04:03:53] Test UFF force-field parameter getters. +130: [04:03:53] ------------------------------------- +130: [04:03:53] Testing handling missing parameters. +130: [04:03:53] UFFTYPER: Unrecognized hybridization for atom: 0 +130: [04:03:53] UFFTYPER: Unrecognized atom type: Cu+1 (0) +115/223 Test #129: testMMFFForceFieldHelpersMultiThread ... Passed 0.95 sec test 135 Start 135: pyDistGeomHelpers 135: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 135: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 135: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -117: pass 1 -117: launch :0 -117: launch :1 -117: launch :2 -117: launch :3 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -106: =>start test rdf custom -106: [07:34:58] test on : 365 molecules done -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -56: Randomness seeded to: 3731930439 -56: =============================================================================== -56: All tests passed (1902 assertions in 21 test cases) -56: -134: Randomness seeded to: 367100113 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [07:34:58] done -128: [07:34:58] ------------------------------------- -128: [07:34:58] Testing Issue242. - 94/223 Test #56: cxsmilesTest ........................... Passed 0.81 sec +130: [04:03:53] UFFTYPER: Unrecognized hybridization for atom: 0 +130: [04:03:53] UFFTYPER: Unrecognized atom type: Cu+1 (0) +130: [04:03:53] done +130: [04:03:53] ------------------------------------- +130: [04:03:53] Testing SFIssue3009337. +130: [04:03:53] done +130: [04:03:53] ------------------------------------- +130: [04:03:53] Test UFF multithreading +134: Randomness seeded to: 2971334454 +130: generating reference data +134: [04:03:53] [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)] +134: [04:03:53] [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)] +134: [04:03:53] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [04:03:53] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [04:03:53] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [04:03:53] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [04:03:53] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [04:03:53] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [04:03:53] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [04:03:53] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [04:03:53] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [04:03:53] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [04:03:53] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [04:03:53] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [04:03:53] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [04:03:53] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [04:03:53] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [04:03:53] [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)] +134: [04:03:53] [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)] +134: [04:03:53] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +134: [04:03:53] [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)] +134: [04:03:53] [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)] +134: [04:03:53] [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)] +134: [04:03:53] [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)] +134: [04:03:53] [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)] +134: [04:03:53] [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)] +134: [04:03:53] [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)] +134: [04:03:53] [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)] +134: [04:03:53] [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)] +134: [04:03:53] [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)] +134: [04:03:53] [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)] +134: [04:03:54] [$([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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +125: ....... +125: ---------------------------------------------------------------------- +125: Ran 7 tests in 0.719s +125: +125: OK +134: [04:03:54] 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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [!#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)] +134: [04:03:54] [!#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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: ----------- +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [$([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)] +134: [04:03:54] [$([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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] 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)] +134: [04:03:54] 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)] +134: [04:03:54] [!#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)] +134: [04:03:54] [!#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)] +134: [04:03:54] [!#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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: ----------- +134: [04:03:54] [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)] +134: [04:03:54] [$([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)] +134: [04:03:54] [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)] +134: [04:03:54] 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)] +134: ----------- +134: ----------- +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [$(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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +134: [04:03:54] [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)] +116/223 Test #125: pyPartialCharges ....................... Passed 2.53 sec test 136 Start 136: testMolAlign 136: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 136: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 136: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -27: ... -27: ---------------------------------------------------------------------- -27: Ran 12 tests in 0.613s -27: -27: OK -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [07:34:58] done -130: [07:34:58] ------------------------------------- -130: [07:34:58] Testing UFF special cases. -130: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 0 -130: [07:34:58] done -130: [07:34:58] ------------------------------------- -130: [07:34:58] Testing Issue239. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -4: dynamic RDValue:0.065841 s -4: deleted! -4: [07:34:58] ------------------------------------- -4: [07:34:58] Testing String Pickle Roundtrips. -4: [07:34:58] done -4: [07:34:58] ------------------------------------- -4: [07:34:58] Testing conversion of vect to string. -4: [07:34:58] done -4: [07:34:58] ------------------------------------- -4: [07:34:58] Testing returning const references. -4: [07:34:58] any cast -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -133: go -4: [07:34:58] done: 0.001349 300000 -4: [07:34:58] copy -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -4: [07:34:58] done: 0.001283 300000 -4: [07:34:58] ref -133: ------------------------------------- -133: -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -4: [07:34:58] done: 0.001275 300000 -4: [07:34:58] dict -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -4: [07:34:58] done: 0.00304 300000 -4: [07:34:58] ref with hasVal -104: 400 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -4: [07:34:58] done: 0.001966 300000 -4: [07:34:58] done -4: [07:34:58] ------------------------------------- -4: [07:34:58] Testing dict update. -4: [07:34:58] done -4: deleted! -4: deleted! -4: deleted! -4: deleted! -4: deleted! -4: deleted! - 95/223 Test #4: testDict ............................... Passed 0.95 sec +106: =>start test 2 WHIM custom +106: [04:03:54] test on : 365 molecules done +134: [04:03:54] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +134: [04:03:54] UFFTYPER: Unrecognized atom type: N_5 (2) +134: [04:03:54] UFFTYPER: Unrecognized atom type: N_5 (3) +134: [04:03:54] UFFTYPER: Unrecognized atom type: N_5 (2) +134: [04:03:54] UFFTYPER: Unrecognized atom type: N_5 (3) +134: [04:03:54] UFFTYPER: Unrecognized charge state for atom: 1 +26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +130: processing +130: launch :0 +130: launch :1 +130: launch :2 +130: launch :3 +130: [04:03:54] Rep: 0 Mol:0 +130: [04:03:54] Rep: 0 Mol:3 +130: [04:03:54] Rep: 0 Mol:2 +134: [04:03:54] UFFTYPER: Unrecognized charge state for atom: 1 +130: [04:03:54] Rep: 0 Mol:4 +130: [04:03:54] Rep: 0 Mol:1 +130: [04:03:54] Rep: 0 Mol:5 +130: [04:03:54] Rep: 0 Mol:9 +134: [04:03:54] UFFTYPER: Unrecognized charge state for atom: 1 +130: [04:03:54] Rep: 0 Mol:8 +130: [04:03:54] Rep: 0 Mol:12 +130: [04:03:54] Rep: 0 Mol:16 +130: [04:03:54] Rep: 0 Mol:13 +130: [04:03:54] Rep: 0 Mol:20 +130: [04:03:54] Rep: 0 Mol:7 +130: [04:03:54] Rep: 0 Mol:11 +130: [04:03:54] Rep: 0 Mol:24 +130: [04:03:54] Rep: 0 Mol:28 +130: [04:03:54] Rep: 0 Mol:6 +130: [04:03:54] Rep: 0 Mol:15 +130: [04:03:54] Rep: 0 Mol:19 +130: [04:03:54] Rep: 0 Mol:10 +130: [04:03:54] Rep: 0 Mol:17 +130: [04:03:54] Rep: 0 Mol:23 +130: [04:03:54] Rep: 0 Mol:27 +130: [04:03:54] Rep: 0 Mol:31 +130: [04:03:55] Rep: 0 Mol:21 +130: [04:03:55] Rep: 0 Mol:14 +130: [04:03:55] Rep: 0 Mol:18 +130: [04:03:55] Rep: 0 Mol:25 +119: [04:03:55] done +119: [04:03:55] ------------------------------------- +119: [04:03:55] Test GitHub Issue #6958 +117/223 Test #119: testFingerprintGenerators .............. Passed 4.49 sec test 137 Start 137: testO3AAlign 137: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 137: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 137: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [07:34:58] done -130: [07:34:58] ------------------------------------- -130: [07:34:58] Testing calcEnergy with passed coords. -112: =>start test autocorr3D -112: [07:34:58] test on : 365 molecules done -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [07:34:58] done -128: [07:34:58] ------------------------------------- -128: [07:34:58] Testing github 308: crash during MMFF parameterization . -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 96/223 Test #62: pyDepictor ............................. Passed 0.82 sec +130: [04:03:55] Rep: 0 Mol:22 +130: [04:03:55] Rep: 0 Mol:26 +130: [04:03:55] Rep: 0 Mol:29 +136: *********************************************************** +136: Testing MolAlign +136: --------------------------------- +136: test1MolAlign +136: +136: --------------------------------- +136: test1GetBestRMS +136: +136: --------------------------------- +136: test1MolWithQueryAlign +136: +136: --------------------------------- +136: test2AtomMap +136: +136: --------------------------------- +136: test3Weights +136: +136: --------------------------------- +136: testIssue241 +136: +136: *********************************************************** +26: All 191 tests passed +118/223 Test #136: testMolAlign ........................... Passed 0.62 sec test 138 Start 138: molAlignCatchTest 138: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 138: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 138: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [07:34:58] ------------------------------------- -103: [07:34:58] Test empty molecule BCUT. -128: [07:34:58] ------------------------------------- -128: [07:34:58] Testing SFIssue1653802. - 97/223 Test #112: testAUTOCORR3D ......................... Passed 0.45 sec +130: [04:03:55] Rep: 0 Mol:30 +132: [04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: [04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: [04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: [04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: [04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: ..[04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: .[04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +119/223 Test #40: resMolSupplierTest ..................... Passed 9.56 sec test 139 Start 139: pyMolAlign 139: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 139: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap 139: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [07:34:58] done -128: [07:34:58] ------------------------------------- -128: [07:34:58] Testing SFIssue2378119. -130: [07:34:58] done -130: [07:34:58] ------------------------------------- -130: [07:34:58] Testing calcGrad. - 98/223 Test #103: testBCUT ............................... Passed 0.61 sec +134: [04:03:55] UFFTYPER: Unrecognized charge state for atom: 5 +132: .[04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +134: [04:03:55] UFFTYPER: Unrecognized charge state for atom: 5 +134: [04:03:55] UFFTYPER: Unrecognized charge state for atom: 5 +132: .[04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +111: =>start test GETAWAY +111: [04:03:55] test on : 365 molecules done +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: .[04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +120/223 Test #111: testGETAWAY ............................ Passed 6.25 sec test 140 Start 140: testFeatures 140: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 140: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures 140: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: [07:34:58] done -128: [07:34:58] ------------------------------------- -128: [07:34:58] Test MMFF force-field parameter getters. -128: [07:34:58] ------------------------------------- -128: [07:34:58] Test MMFF multithreading -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 99/223 Test #131: testCrystalForceField .................. Passed 0.19 sec -test 141 - Start 141: pyChemicalFeatures - -141: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" -141: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap -141: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [07:34:58] done -130: [07:34:58] ------------------------------------- -130: [07:34:58] Testing SFIssue1653802. -130: [07:34:58] done -130: [07:34:58] ------------------------------------- -130: [07:34:58] Testing SFIssue2378119. -130: [07:34:58] done -130: [07:34:58] ------------------------------------- -130: [07:34:58] Test UFF force-field parameter getters. -130: [07:34:58] ------------------------------------- -130: [07:34:58] Testing handling missing parameters. -130: [07:34:58] UFFTYPER: Unrecognized hybridization for atom: 0 -130: [07:34:58] UFFTYPER: Unrecognized atom type: Cu+1 (0) -130: [07:34:58] UFFTYPER: Unrecognized hybridization for atom: 0 -130: [07:34:58] UFFTYPER: Unrecognized atom type: Cu+1 (0) -140: [07:34:58] ------------------------------------- -140: [07:34:58] AtomType parser testing. -140: [07:34:58] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -140: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -140: [07:34:58] done -140: [07:34:58] ------------------------------------- -140: [07:34:58] FeatureDefinition parser testing. -140: [07:34:58] done -140: [07:34:58] ------------------------------------- -140: [07:34:58] Test pulling feat defs from a string. -140: [07:34:58] done -140: [07:34:58] ------------------------------------- -140: [07:34:58] FeatureDef functionality testing. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -128: generating reference data -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: [07:34:58] done -130: [07:34:58] ------------------------------------- -130: [07:34:58] Testing SFIssue3009337. -130: [07:34:58] done -130: [07:34:58] ------------------------------------- -130: [07:34:58] Test UFF multithreading -140: [07:34:58] done -140: [07:34:58] ------------------------------------- -140: [07:34:58] FeatureFactory testing. -140: [07:34:58] 1 -140: [07:34:58] 2 -140: [07:34:58] 3 -140: [07:34:58] 4 -140: [07:34:58] 5 -140: [07:34:58] 6 -140: [07:34:58] done -140: [07:34:58] ------------------------------------- -140: [07:34:58] Feature Location testing. -140: [07:34:58] done -140: [07:34:58] ------------------------------------- -140: [07:34:58] Test building a FeatureFactory from a file -140: [07:34:58] done -140: [07:34:58] ------------------------------------- -140: [07:34:58] Testing Issue 224. -140: [07:34:58] done -140: [07:34:58] ------------------------------------- -140: [07:34:58] Testing Issue 225. -140: [07:34:58] done -140: [07:34:58] ------------------------------------- -140: [07:34:58] Test Issue346 -140: [07:34:58] done -140: [07:34:58] ------------------------------------- -140: [07:34:58] Test Issue347 -140: [07:34:58] done -140: [07:34:58] ------------------------------------- -140: [07:34:58] Testing Issue 348. -140: [07:34:58] SMARTS Parse Error: syntax error while parsing: [C[C] -140: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -140: [07:34:58] ------------------------------------- -140: [07:34:58] Testing Nested AtomType definitions. +132: .[04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +140: [04:03:55] ------------------------------------- +140: [04:03:55] AtomType parser testing. +140: [04:03:55] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +140: [04:03:55] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' +140: [04:03:55] done +140: [04:03:55] ------------------------------------- +140: [04:03:55] FeatureDefinition parser testing. +140: [04:03:55] done +140: [04:03:55] ------------------------------------- +140: [04:03:55] Test pulling feat defs from a string. +140: [04:03:55] done +140: [04:03:55] ------------------------------------- +140: [04:03:55] FeatureDef functionality testing. +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: ..[04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +26: +26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +140: [04:03:55] done +140: [04:03:55] ------------------------------------- +140: [04:03:55] FeatureFactory testing. +132: .[04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: .[04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: .[04:03:55] UFFTYPER: Unrecognized hybridization for atom: 0 +132: [04:03:55] UFFTYPER: Unrecognized atom type: Cu+1 (0) +132: .[04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +140: [04:03:55] 1 +140: [04:03:55] 2 +140: [04:03:55] 3 +140: [04:03:55] 4 +140: [04:03:55] 5 +140: [04:03:55] 6 +140: [04:03:55] done +140: [04:03:55] ------------------------------------- +140: [04:03:55] Feature Location testing. +140: [04:03:55] done +140: [04:03:55] ------------------------------------- +140: [04:03:55] Test building a FeatureFactory from a file +140: [04:03:55] done +140: [04:03:55] ------------------------------------- +140: [04:03:55] Testing Issue 224. +140: [04:03:55] done +140: [04:03:55] ------------------------------------- +140: [04:03:55] Testing Issue 225. +140: [04:03:55] done +140: [04:03:55] ------------------------------------- +140: [04:03:55] Test Issue346 +140: [04:03:55] done +140: [04:03:55] ------------------------------------- +140: [04:03:55] Test Issue347 +140: [04:03:55] done +140: [04:03:55] ------------------------------------- +140: [04:03:55] Testing Issue 348. +140: [04:03:55] SMARTS Parse Error: syntax error while parsing: [C[C] +140: [04:03:55] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +140: [04:03:55] ------------------------------------- +140: [04:03:55] Testing Nested AtomType definitions. 140: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -140: [07:34:58] ------------------------------------- -140: [07:34:58] Testing Github Issue #252: crash when calling getPos() with no conformer. -140: [07:34:58] expect a precondition failure message below -140: [07:34:58] +140: [04:03:55] ------------------------------------- +140: [04:03:55] Testing Github Issue #252: crash when calling getPos() with no conformer. +140: [04:03:55] expect a precondition failure message below +140: [04:03:55] 140: 140: **** 140: Pre-condition Violation @@ -19723,141 +20415,155 @@ 140: Failed Expression: dp_mol->getNumConformers() 140: **** 140: -140: [07:34:58] Done -140: [07:34:58] ------------------------------------- -140: [07:34:58] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -140: [07:34:58] done -100/223 Test #140: testFeatures ........................... Passed 0.03 sec +140: [04:03:55] Done +140: [04:03:55] ------------------------------------- +140: [04:03:55] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +140: [04:03:55] done +132: [04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: [04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: [04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: [04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: .[04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: .[04:03:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: .[04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: ..[04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +121/223 Test #140: testFeatures ........................... Passed 0.17 sec +test 141 + Start 141: pyChemicalFeatures + +141: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" +141: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap +141: Test timeout computed to be: 1500 +132: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: ..[04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +128: processing +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +128: [04:03:55] Rep: 0 Mol:2 +128: [04:03:55] Rep: 0 Mol:3 +128: [04:03:55] Rep: 0 Mol:0 +128: [04:03:55] Rep: 0 Mol:1 +135: .[04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:55] Rep: 0 Mol:5 +132: ... +132: ---------------------------------------------------------------------- +132: Ran 18 tests in 0.655s +132: +132: OK +106: =>start test 1 WHIM custom +106: [04:03:55] test on : 365 molecules done +128: [04:03:55] Rep: 0 Mol:4 +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:55] Rep: 0 Mol:9 +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:55] Rep: 0 Mol:13 +130: [04:03:55] Rep: 100 Mol:0 +130: [04:03:55] Rep: 100 Mol:4 +130: [04:03:55] Rep: 100 Mol:8 +130: [04:03:55] Rep: 100 Mol:12 +130: [04:03:55] Rep: 100 Mol:16 +130: [04:03:55] Rep: 100 Mol:20 +138: Randomness seeded to: 4248183180 +138: 508356180 +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:55] Rep: 0 Mol:6 +130: [04:03:55] Rep: 100 Mol:24 +130: [04:03:55] Rep: 100 Mol:28 +128: [04:03:55] Rep: 0 Mol:8 +128: [04:03:55] Rep: 0 Mol:10 +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:55] Rep: 0 Mol:12 +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:55] Rep: 0 Mol:7 +128: [04:03:55] Rep: 0 Mol:17 +128: [04:03:55] Rep: 0 Mol:11 +134: [04:03:55] UFFTYPER: Unrecognized charge state for atom: 6 +128: [04:03:55] Rep: 0 Mol:16 +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:55] Rep: 0 Mol:15 +128: [04:03:55] Rep: 0 Mol:19 +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:55] Rep: 0 Mol:23 +128: [04:03:55] Rep: 0 Mol:27 +130: [04:03:55] Rep: 100 Mol:3 +130: [04:03:55] Rep: 100 Mol:7 +130: [04:03:55] Rep: 100 Mol:11 +130: [04:03:55] Rep: 100 Mol:15 +130: [04:03:55] Rep: 100 Mol:19 +130: [04:03:55] Rep: 100 Mol:23 +130: [04:03:55] Rep: 100 Mol:27 +130: [04:03:55] Rep: 100 Mol:31 +128: [04:03:55] Rep: 0 Mol:20 +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:55] Rep: 0 Mol:31 +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +134: [04:03:55] UFFTYPER: Unrecognized charge state for atom: 6 +128: [04:03:55] Rep: 0 Mol:24 +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:55] Rep: 0 Mol:28 +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +122/223 Test #132: pyForceFieldHelpers .................... Passed 2.59 sec test 142 Start 142: testShapeHelpers 142: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 142: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers 142: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -130: generating reference data -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -134: [07:34:58] [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)] -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test unfolded version of RDKFP -134: [07:34:58] [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)] -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test topological torsion fp generator -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -134: [07:34:58] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [07:34:58] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [07:34:58] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [07:34:58] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [07:34:58] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [07:34:58] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [07:34:58] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [07:34:58] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [07:34:58] [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)] -107: =>start test rdf -107: [07:34:58] test on : 365 molecules done -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -134: [07:34:58] [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)] -134: [07:34:58] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test Topological Torsions. -101/223 Test #107: testRDF ................................ Passed 0.66 sec -test 143 - Start 143: pyShapeHelpers - -143: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" -143: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap -143: Test timeout computed to be: 1500 -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test Folded torsions. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test Bulk Topological Torsions. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -134: [07:34:58] [$([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)] -134: [07:34:58] [$(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)] -134: [07:34:58] [$(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)] -134: [07:34:58] [$(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)] -134: [07:34:58] [$(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)] -134: [07:34:58] [$(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)] -134: [07:34:58] [$(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)] -134: [07:34:58] [$(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)] -134: [07:34:58] [$(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)] -123: .. -123: ---------------------------------------------------------------------- -123: Ran 2 tests in 0.035s -123: -123: OK -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -134: [07:34:58] [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)] -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -134: [07:34:58] [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)] +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:55] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:56] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:56] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:56] Rep: 0 Mol:21 +134: [04:03:56] UFFTYPER: Unrecognized charge state for atom: 6 +135: [04:03:56] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:56] Rep: 0 Mol:14 +128: [04:03:56] Rep: 0 Mol:25 142: *********************************************************** 142: Testing ShapeHelpers 142: --------------------------------- @@ -19870,333 +20576,512 @@ 142: testGithub4364 142: 142: *********************************************************** -102/223 Test #27: pyForceFieldConstraints ................ Passed 1.03 sec -103/223 Test #142: testShapeHelpers ....................... Passed 0.07 sec +123/223 Test #142: testShapeHelpers ....................... Passed 0.11 sec +test 143 + Start 143: pyShapeHelpers + +143: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" +143: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap +143: Test timeout computed to be: 1500 +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 10.506s +12: +12: OK +128: [04:03:56] Rep: 0 Mol:18 +128: [04:03:56] Rep: 0 Mol:29 +128: [04:03:56] Rep: 0 Mol:22 +135: [04:03:56] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:56] Rep: 0 Mol:26 +128: [04:03:56] Rep: 0 Mol:30 +124/223 Test #12: pyBV ................................... Passed 11.05 sec test 144 Start 144: testMolCatalog 144: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 144: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog 144: Test timeout computed to be: 1500 +135: [04:03:56] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:56] Rep: 20 Mol:3 +128: [04:03:56] Rep: 20 Mol:7 +128: [04:03:56] Rep: 20 Mol:11 +128: [04:03:56] Rep: 20 Mol:15 +128: [04:03:56] Rep: 20 Mol:19 +128: [04:03:56] Rep: 20 Mol:23 +128: [04:03:56] Rep: 20 Mol:27 +128: [04:03:56] Rep: 20 Mol:31 +138: 502726322 +135: [04:03:56] Molecule does not have explicit Hs. Consider calling AddHs() +125/223 Test #144: testMolCatalog ......................... Passed 0.12 sec test 145 Start 145: pyMolCatalog 145: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 145: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 145: Test timeout computed to be: 1500 -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: Elapsed time: 0.676973 s -104: Errors:0 -104: [07:34:58] test on : 500 molecules done -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] 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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [!#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)] -134: [07:34:58] [!#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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: ----------- -115: .....[07:34:58] -115: -115: **** -115: Pre-condition Violation -115: Number of atom props not equal to number of atoms -115: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp -115: Failed Expression: atom_props.size() == num_atoms -115: **** -115: -136: *********************************************************** -136: Testing MolAlign -136: --------------------------------- -136: test1MolAlign -136: -136: --------------------------------- -136: test1GetBestRMS -136: -136: --------------------------------- -136: test1MolWithQueryAlign -136: -136: --------------------------------- -136: test2AtomMap -136: -136: --------------------------------- -136: test3Weights -136: -136: --------------------------------- -136: testIssue241 -136: -136: *********************************************************** -104/223 Test #104: testEEM ................................ Passed 0.71 sec -105/223 Test #136: testMolAlign ........................... Passed 0.15 sec +128: [04:03:56] Rep: 20 Mol:0 +128: [04:03:56] Rep: 20 Mol:4 +128: [04:03:56] Rep: 20 Mol:8 +128: [04:03:56] Rep: 20 Mol:12 +135: [04:03:56] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:56] Rep: 20 Mol:16 +128: [04:03:56] Rep: 20 Mol:20 +128: [04:03:56] Rep: 20 Mol:24 +128: [04:03:56] Rep: 20 Mol:28 +135: [04:03:56] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:56] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:56] Rep: 40 Mol:3 +128: [04:03:56] Rep: 40 Mol:7 +128: [04:03:56] Rep: 40 Mol:11 +128: [04:03:56] Rep: 40 Mol:15 +128: [04:03:56] Rep: 40 Mol:19 +128: [04:03:56] Rep: 40 Mol:23 +128: [04:03:56] Rep: 40 Mol:27 +128: [04:03:56] Rep: 40 Mol:31 +135: [04:03:56] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:56] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:56] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:56] Rep: 60 Mol:3 +128: [04:03:56] Rep: 20 Mol:1 +128: [04:03:56] Rep: 20 Mol:5 +128: [04:03:56] Rep: 20 Mol:9 +128: [04:03:56] Rep: 20 Mol:13 +128: [04:03:56] Rep: 20 Mol:17 +128: [04:03:56] Rep: 60 Mol:7 +128: [04:03:56] Rep: 20 Mol:21 +128: [04:03:56] Rep: 60 Mol:11 +128: [04:03:56] Rep: 20 Mol:25 +128: [04:03:56] Rep: 60 Mol:15 +128: [04:03:56] Rep: 60 Mol:19 +128: [04:03:56] Rep: 60 Mol:23 +128: [04:03:56] Rep: 60 Mol:27 +128: [04:03:56] Rep: 60 Mol:31 +128: [04:03:56] Rep: 20 Mol:29 +135: [04:03:56] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:57] Rep: 40 Mol:0 +128: [04:03:57] Rep: 40 Mol:4 +128: [04:03:57] Rep: 40 Mol:8 +128: [04:03:57] Rep: 40 Mol:12 +128: [04:03:57] Rep: 40 Mol:16 +128: [04:03:57] Rep: 40 Mol:20 +128: [04:03:57] Rep: 40 Mol:24 +128: [04:03:57] Rep: 40 Mol:28 +135: [04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:03:57] Rep: 20 Mol:2 +128: [04:03:57] Rep: 20 Mol:6 +128: [04:03:57] Rep: 20 Mol:10 +128: [04:03:57] Rep: 80 Mol:3 +128: [04:03:57] Rep: 80 Mol:7 +128: [04:03:57] Rep: 20 Mol:14 +128: [04:03:57] Rep: 80 Mol:11 +128: [04:03:57] Rep: 20 Mol:18 +128: [04:03:57] Rep: 80 Mol:15 +128: [04:03:57] Rep: 20 Mol:22 +128: [04:03:57] Rep: 80 Mol:19 +128: [04:03:57] Rep: 20 Mol:26 +128: [04:03:57] Rep: 80 Mol:23 +128: [04:03:57] Rep: 80 Mol:27 +128: [04:03:57] Rep: 80 Mol:31 +128: [04:03:57] Rep: 20 Mol:30 +135: [04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +145: . +145: ---------------------------------------------------------------------- +145: Ran 1 test in 0.055s +145: +145: OK +141: .[04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +143: . +143: ---------------------------------------------------------------------- +143: Ran 1 test in 0.390s +143: +143: OK +143: Testing Shape Helpers wrapper +135: [04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +141: .[04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +130: [04:03:57] Rep: 100 Mol:1 +130: [04:03:57] Rep: 100 Mol:5 +130: [04:03:57] Rep: 100 Mol:9 +130: [04:03:57] Rep: 100 Mol:13 +130: [04:03:57] Rep: 100 Mol:17 +130: [04:03:57] Rep: 100 Mol:21 +130: [04:03:57] Rep: 100 Mol:25 +130: [04:03:57] Rep: 100 Mol:29 +135: [04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +130: [04:03:57] Rep: 100 Mol:2 +130: [04:03:57] Rep: 100 Mol:6 +130: [04:03:57] Rep: 100 Mol:10 +135: [04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +130: [04:03:57] Rep: 100 Mol:14 +130: [04:03:57] Rep: 100 Mol:18 +130: [04:03:57] Rep: 100 Mol:22 +130: [04:03:57] Rep: 100 Mol:26 +130: [04:03:57] Rep: 100 Mol:30 +135: .[04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +141: ..[04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +126/223 Test #143: pyShapeHelpers ......................... Passed 1.44 sec test 146 Start 146: moldraw2DTest1 146: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 146: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 146: Test timeout computed to be: 1500 +141: .[04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +141: .[04:03:57] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +141: [04:03:57] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +141: ... +141: ---------------------------------------------------------------------- +141: Ran 9 tests in 0.351s +141: +141: OK +128: [04:03:57] Rep: 40 Mol:1 +128: [04:03:57] Rep: 40 Mol:5 +128: [04:03:57] Rep: 40 Mol:9 +128: [04:03:57] Rep: 40 Mol:13 +128: [04:03:57] Rep: 40 Mol:17 +127/223 Test #145: pyMolCatalog ........................... Passed 1.24 sec test 147 Start 147: moldraw2DTestCatch 147: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 147: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 147: Test timeout computed to be: 1500 -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [$([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)] -134: [07:34:58] [$([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)] -134: [07:34:58] [$(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)] -134: [07:34:58] [$(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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] 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)] -134: [07:34:58] 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)] -134: [07:34:58] [!#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)] -134: [07:34:58] [!#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)] -134: [07:34:58] [!#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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: ----------- -134: [07:34:58] [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)] -134: [07:34:58] [$([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)] -134: [07:34:58] [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)] -134: [07:34:58] 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)] -106/223 Test #144: testMolCatalog ......................... Passed 0.04 sec +146: ----------------- Test 1 +128: [04:03:57] Rep: 60 Mol:0 +128: [04:03:57] Rep: 40 Mol:21 +128: [04:03:57] Rep: 60 Mol:4 +128: [04:03:57] Rep: 40 Mol:25 +128: [04:03:57] Rep: 40 Mol:29 +128: [04:03:57] Rep: 60 Mol:8 +128: [04:03:57] Rep: 60 Mol:12 +128: [04:03:57] Rep: 60 Mol:16 +128: [04:03:57] Rep: 60 Mol:20 +128: [04:03:57] Rep: 60 Mol:24 +128: [04:03:57] Rep: 60 Mol:28 +146: file test1_5.svg gave hash 2383324771U not the expected 2811480876U +147: Randomness seeded to: 639571488 +147: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U +146: Done +146: ----------------- Test 2 +128/223 Test #141: pyChemicalFeatures ..................... Passed 2.08 sec test 148 Start 148: moldraw2DRxnTest1 148: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 148: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 148: Test timeout computed to be: 1500 -134: ----------- -107/223 Test #123: pyTestMHFP ............................. Passed 0.41 sec +146: file test2_1.png gave hash 1188732611U not the expected 307437906U +146: file test2_2.png gave hash 206445131U not the expected 610424244U +135: [04:03:57] Molecule does not have explicit Hs. Consider calling AddHs() +148: ----------------- Test 1 +146: Done +146: ----------------- Test 4 +147: file contourMol_1.svg gave hash 4125787245U not the expected 2604538953U +146: file test4_1.png gave hash 297807158U not the expected 1403972924U +146: Done +146: ----------------- Test 5 +147: file contourMol_2.svg gave hash 2850811663U not the expected 572669511U +146: file test5_1.png gave hash 1384886438U not the expected 1269428339U +146: file test5_2.png gave hash 3891642937U not the expected 3073694291U +147: file contourMol_3.svg gave hash 1894450507U not the expected 936771429U +147: file contourMol_4.svg gave hash 1717526955U not the expected 3302971362U +148: file rxn_test1_1.png gave hash 1121707892U not the expected 1556334749U +146: file test5_3.png gave hash 442326768U not the expected 1865192682U +146: Done +146: ----------------- Test 6 (atom labels) +147: file contourMol_5.svg gave hash 1093404576U not the expected 2230414999U +146: Done +146: ----------------- Test 7 (backgrounds) +146: file test7_1.png gave hash 2325902062U not the expected 3033050306U +128: [04:03:58] Rep: 40 Mol:2 +146: file test7_2.png gave hash 3963123595U not the expected 3476380724U +146: Done +146: ----------------- Test8: PrepareMolDrawing +146: Done +146: ----------------- Test multi-threaded drawing +146: reading molecules +128: [04:03:58] Rep: 40 Mol:6 +128: [04:03:58] Rep: 40 Mol:10 +128: [04:03:58] Rep: 40 Mol:14 +128: [04:03:58] Rep: 40 Mol:18 +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test Issue252: Bad definitions for Crippen atom types. +128: [04:03:58] Rep: 40 Mol:22 +128: [04:03:58] Rep: 40 Mol:26 +128: [04:03:58] Rep: 40 Mol:30 +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test calculation of ChiVs. +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test calculation of ChiNs. +146: generating reference drawings +148: file rxn_test1_2.png gave hash 1557885590U not the expected 1924084263U +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test calculation of HallKierAlpha. +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test calculation of Kappa1. +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test calculation of Kappa2. +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test calculation of Kappa3. +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test Crippen atom type calculations. +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test ring descriptors +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test other count descriptors. +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test MQN +147: file testGithub3226_1.png gave hash 1140467476U not the expected 2350054896U +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test GitHub Issue 56. +100: [04:03:58] WARNING: not removing hydrogen atom without neighbors +100: [04:03:58] WARNING: not removing hydrogen atom without neighbors +100: [04:03:58] WARNING: not removing hydrogen atom without neighbors +100: [04:03:58] WARNING: not removing hydrogen atom without neighbors +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test Github92: Bad Crippen atom type for pyrrole H. +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test Github362: order dependence in Kier-Hall descriptors. +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test calculation of spiro and bridgehead counts. +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test Github694: ExactMolWt ignoring the mass of the electron +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Testing Properties and KitchenSink +100: [04:03:58] ---Caught keyerror (bad property name)--- +100: [04:03:58] ---Caught stereo value error--- +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test USR Descriptor +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test Github #1973: support P and S terms for TPSA calculation +100: [04:03:58] done +100: [04:03:58] ------------------------------------- +100: [04:03:58] Test Github #2948: Empty molecule has non-zero LabuteASA +100: [04:03:58] done +147: file testGithub3226_2.png gave hash 1788850357U not the expected 606206725U +129/223 Test #100: testDescriptors ........................ Passed 10.40 sec test 149 Start 149: pyMolDraw2D 149: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" 149: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap 149: Test timeout computed to be: 1500 -129: done -98: [07:34:58] -98: -98: **** -98: Invariant Violation -98: nonsense -98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -98: Failed Expression: token != tokens.end() -98: **** -98: -98: [07:34:58] -98: -98: **** -115: ......................... -115: ---------------------------------------------------------------------- -115: Ran 30 tests in 0.054s -115: -98: Invariant Violation -98: nonsense no new line -98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -98: Failed Expression: token != tokens.end() -98: **** -98: -98: [07:34:58] -98: -98: **** -98: Invariant Violation -98: nonsense with tab -98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -98: Failed Expression: token != tokens.end() -98: **** -98: -115: OK -115: exactmw 78.046950192 -115: amw 78.11399999999999 -115: lipinskiHBA 0.0 -115: lipinskiHBD 0.0 -115: NumRotatableBonds 0.0 -115: NumHBD 0.0 -115: NumHBA 0.0 -115: NumHeavyAtoms 6.0 -115: NumAtoms 6.0 -115: NumHeteroatoms 0.0 -115: NumAmideBonds 0.0 -115: FractionCSP3 0.0 -115: NumRings 1.0 -115: NumAromaticRings 1.0 -115: NumAliphaticRings 0.0 -115: NumSaturatedRings 0.0 -115: NumHeterocycles 0.0 -115: NumAromaticHeterocycles 0.0 -115: NumSaturatedHeterocycles 0.0 -115: NumAliphaticHeterocycles 0.0 -115: NumSpiroAtoms 0.0 -115: NumBridgeheadAtoms 0.0 -115: NumAtomStereoCenters 0.0 -115: NumUnspecifiedAtomStereoCenters 0.0 -115: labuteASA 37.43140311949697 -115: tpsa 0.0 -115: CrippenClogP 1.6866 -115: CrippenMR 26.441999999999993 -115: chi0v 3.464101615137755 -115: chi1v 2.0000000000000004 -115: chi2v 0.6666666666666671 -115: chi3v 0.6666666666666671 -115: chi4v 0.38490017945975075 -115: chi0n 3.464101615137755 -115: chi1n 2.0000000000000004 -115: chi2n 0.6666666666666671 -115: chi3n 0.6666666666666671 -115: chi4n 0.38490017945975075 -115: hallKierAlpha -0.78 -115: kappa1 3.4115708812260532 -115: kappa2 1.6057694396735218 -115: kappa3 0.5823992601400448 -115: Phi 0.9130327103921437 -115: exactmw 78.046950192 -115: lipinskiHBA 0.0 -134: ----------- -108/223 Test #98: testFragCatalog ........................ Passed 0.78 sec +148: file rxn_test1_3.png gave hash 3006127285U not the expected 1644921059U +128: [04:03:58] Rep: 60 Mol:1 +128: [04:03:58] Rep: 60 Mol:5 +128: [04:03:58] Rep: 60 Mol:9 +128: [04:03:58] Rep: 60 Mol:13 +128: [04:03:58] Rep: 60 Mol:17 +128: [04:03:58] Rep: 60 Mol:21 +128: [04:03:58] Rep: 60 Mol:25 +147: file testGithub3226_3.png gave hash 2180602679U not the expected 2282880418U +128: [04:03:58] Rep: 60 Mol:29 +128: [04:03:58] Rep: 80 Mol:0 +147: file testPNGMetadata_1.png gave hash 3955478692U not the expected 2423299691U +128: [04:03:58] Rep: 80 Mol:4 +128: [04:03:58] Rep: 80 Mol:8 +128: [04:03:58] Rep: 80 Mol:12 +128: [04:03:58] Rep: 80 Mol:16 +128: [04:03:58] Rep: 80 Mol:20 +128: [04:03:58] Rep: 80 Mol:24 +128: [04:03:58] Rep: 80 Mol:28 +148: file rxn_test1_4.png gave hash 326223573U not the expected 2471435686U +146: processing +146: launch :0 +146: launch :1 +146: launch :2 +146: launch :3 +148: file rxn_test1_5.png gave hash 1915733777U not the expected 1428782307U +147: file testPNGMetadata_2.png gave hash 1862211480U not the expected 2803353117U +148: file rxn_test1_6.png gave hash 793678174U not the expected 483353696U +147: file testGithub3369_1.svg gave hash 1012801087U not the expected 3091976328U +148: file rxn_test1_7.png gave hash 1232578493U not the expected 528963379U +148: file rxn_test1_7.svg gave hash 798375802U not the expected 1881564163U +148: Done +148: ----------------- Test 2: some examples that caused problems in testing +128: [04:03:58] Rep: 60 Mol:2 +128: [04:03:58] Rep: 60 Mol:6 +128: [04:03:58] Rep: 60 Mol:10 +148: file rxn_test2_1.png gave hash 160703765U not the expected 399415052U +128: [04:03:58] Rep: 60 Mol:14 +128: [04:03:58] Rep: 60 Mol:18 +128: [04:03:58] Rep: 60 Mol:22 +128: [04:03:58] Rep: 60 Mol:26 +128: [04:03:59] Rep: 60 Mol:30 +135: [04:03:59] Molecule does not have explicit Hs. Consider calling AddHs() +147: [04:03:59] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [04:03:59] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +148: 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 +130: [04:03:59] done +130: [04:03:59] ------------------------------------- +130: [04:03:59] Test UFF multithreading2 +148: file rxn_test2_2_1.png gave hash 4057570363U not the expected 1215378243U +128: [04:03:59] Rep: 80 Mol:1 +147: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U +147: [04:03:59] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [04:03:59] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +128: [04:03:59] Rep: 80 Mol:5 +128: [04:03:59] Rep: 80 Mol:9 +128: [04:03:59] Rep: 80 Mol:13 +128: [04:03:59] Rep: 80 Mol:17 +148: 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 +128: [04:03:59] Rep: 80 Mol:21 +128: [04:03:59] Rep: 80 Mol:25 +128: [04:03:59] Rep: 80 Mol:29 +148: file rxn_test2_2_2.png gave hash 362458924U not the expected 3645141778U +148: 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 +148: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl +148: 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 +147: file testHandDrawn-1.png gave hash 811421521U not the expected 698316547U +148: file rxn_test2_2_3.png gave hash 1657316579U not the expected 551946805U +148: 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: file rxn_test2_2_4.png gave hash 2796626100U not the expected 4234617566U +64: [04:03:59] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +64: [04:03:59] 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: Done +148: ----------------- Test 3: test reactant highlighting +148: file rxn_test3_1.png gave hash 3699939964U not the expected 4176857511U +148: file rxn_test3_1.svg gave hash 1959543526U not the expected 2165658826U +148: Done +148: ----------------- Test 4: some examples from SMARTS in testing +148: draw! +147: [04:03:59] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [04:03:59] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +147: file testHandDrawn-2.svg gave hash 2224670338U not the expected 4132716144U +147: [04:03:59] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [04:03:59] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +134: [04:03:59] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: file rxn_test4_1.png gave hash 1897728811U not the expected 4187207676U +148: file rxn_test4_1.svg gave hash 2683567127U not the expected 3239755313U +148: done +149: ...[04:03:59] Font file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +149: [04:03:59] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +147: file testHandDrawn-2.png gave hash 928126416U not the expected 1605553248U +147: [04:04:00] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [04:04:00] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +64: ---------------------------------- +64: ---------------------------------- +64: [04:04:00] +64: +64: **** +64: Pre-condition Violation +64: rlabel out of range for MDL files +64: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp +64: Failed Expression: rlabel >= 0 && rlabel < 100 +64: **** +64: +64: [04:04:00] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +147: file testHandDrawn-3.svg gave hash 633044862U not the expected 4199337510U +147: [04:04:00] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [04:04:00] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +67: [04:04:00] Finished: testSmiCorrectness() +67: [04:04:00] ----------------------------------------- +67: +67: [04:04:00] +67: ----------------------------------------- +148: file rxn_test4_2.png gave hash 3724924058U not the expected 3490081297U +147: file testHandDrawn-3.png gave hash 2410179907U not the expected 2881952238U +67: [04:04:00] Spurious data before the first property will be ignored +67: [04:04:00] Property will be truncated after the first blank line +67: [04:04:00] Property will be truncated after the first blank line +67: [04:04:00] Property will be truncated after the first blank line +148: file rxn_test4_2.svg gave hash 4278906476U not the expected 4127054729U +148: Done +149: ..........[04:04:00] +149: +149: **** +149: Pre-condition Violation +149: molecule must not be None +149: Violation occurred on line 432 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp +149: Failed Expression: m +149: **** +149: +130/223 Test #148: moldraw2DRxnTest1 ...................... Passed 2.45 sec test 150 Start 150: testFMCS 150: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/testFMCS 150: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS 150: Test timeout computed to be: 1500 -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [$(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)] -134: [07:34:58] [$(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)] -134: [07:34:58] [$(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)] -134: [07:34:58] [$(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)] -134: [07:34:58] [$(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)] -134: [07:34:58] [$(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)] -138: Randomness seeded to: 118416601 -138: 112543012 -146: ----------------- Test 1 -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -134: [07:34:58] [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)] -129: [07:34:58] done -148: ----------------- Test 1 -127: ........ -127: ---------------------------------------------------------------------- -127: Ran 8 tests in 0.034s -127: -127: OK -147: Randomness seeded to: 2597391031 -147: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U -146: file test1_5.svg gave hash 2383324771U not the expected 2811480876U -146: Done -146: ----------------- Test 2 -109/223 Test #129: testMMFFForceFieldHelpersMultiThread ... Passed 0.41 sec +147: [04:04:00] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [04:04:00] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +128: [04:04:00] Rep: 80 Mol:2 +128: [04:04:00] Rep: 80 Mol:6 +128: [04:04:00] Rep: 80 Mol:10 +128: [04:04:00] Rep: 80 Mol:14 +128: [04:04:00] Rep: 80 Mol:18 +147: file testHandDrawn-4.svg gave hash 2180320567U not the expected 4197407865U +147: [04:04:00] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [04:04:00] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +128: [04:04:00] Rep: 80 Mol:22 +128: [04:04:00] Rep: 80 Mol:26 +128: [04:04:00] Rep: 80 Mol:30 +147: file testHandDrawn-4.png gave hash 1714306199U not the expected 3431655453U +134: [04:04:00] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +135: [04:04:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [04:04:00] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +130: [04:04:00] done +130: [04:04:00] ------------------------------------- +130: [04:04:00] Test UFF multithreading3 +149: ..................... +149: ---------------------------------------------------------------------- +149: Ran 34 tests in 1.050s +149: +149: OK +149: json lasso +128: [04:04:01] done +128: [04:04:01] ------------------------------------- +128: [04:04:01] Test MMFF multithreading2 +64: [04:04:01] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +64: [04:04:01] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +134: [04:04:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +131/223 Test #149: pyMolDraw2D ............................ Passed 3.24 sec test 151 Start 151: pyFMCS 151: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/testFMCS.py" 151: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap 151: Test timeout computed to be: 1500 -146: file test2_1.png gave hash 1188732611U not the expected 307437906U -148: file rxn_test1_1.png gave hash 1121707892U not the expected 1556334749U -110/223 Test #115: pyMolDescriptors ....................... Passed 0.61 sec +134: [04:04:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +67: [04:04:01] Finished: testSDCorrectness() +67: [04:04:01] ----------------------------------------- +67: +132/223 Test #67: testMultithreadedMolSupplier ........... Passed 15.40 sec test 152 Start 152: FMCStest 152: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 152: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test 152: Test timeout computed to be: 1500 -146: file test2_2.png gave hash 206445131U not the expected 610424244U -122: ............. -122: ---------------------------------------------------------------------- -122: Ran 13 tests in 0.181s -122: -122: OK -117: pass 2 -117: launch :0 -117: launch :1 -117: launch :2 -117: launch :3 -147: file contourMol_1.svg gave hash 4125787245U not the expected 2604538953U -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test Rooted Topological Torsions. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test ignoring atoms in Topological Torsions. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test Topological Torsions including info about chirality. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test GitHub Issue 25: fingerprint backwards compatibility. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -111/223 Test #127: pyMolTransforms ........................ Passed 0.46 sec -test 153 - Start 153: molHashCatchTest - -153: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest -153: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash -153: Test timeout computed to be: 1500 -64: [07:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [07:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [07:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [07:34:58] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [07:34:58] deprecated group abbreviation ignored on line 24 -64: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -64: [07:34:58] -64: -64: **** -64: Post-condition Violation -64: Element 'Mv' not found -64: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -64: Failed Expression: anum > -1 -64: **** -64: -147: file contourMol_2.svg gave hash 2850811663U not the expected 572669511U -146: Done -146: ----------------- Test 4 -119: [07:34:58] done -119: [07:34:58] ------------------------------------- -119: [07:34:58] Test convenience and bulk fp calculation functions -116: ........ -116: ---------------------------------------------------------------------- -116: Ran 8 tests in 0.205s -116: -116: OK -148: file rxn_test1_2.png gave hash 1557885590U not the expected 1924084263U -138: 84897061 -33: [07:34:58] Maximum BFS search size exceeded. -33: This is likely due to a highly symmetric fused ring system. -146: file test4_1.png gave hash 297807158U not the expected 1403972924U -146: Done -146: ----------------- Test 5 -147: file contourMol_3.svg gave hash 1894450507U not the expected 936771429U -147: file contourMol_4.svg gave hash 1717526955U not the expected 3302971362U +64: [04:04:01] Empty atom list: 'M ALS 1 0 F' on line 8. +64: de_DE.UTF-8 +64: [04:04:01] ------------------------------------- +64: [04:04:01] Test multithreading Locale Switching +134: [04:04:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory @@ -21913,18 +22798,6 @@ 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory -147: file contourMol_5.svg gave hash 1093404576U not the expected 2230414999U -132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -132: ..[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory @@ -22174,106 +23047,83 @@ 152: 152: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 152: ERROR: RDKit could not load input file -146: file test5_1.png gave hash 1384886438U not the expected 1269428339U -148: file rxn_test1_3.png gave hash 3006127285U not the expected 1644921059U -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112/223 Test #152: FMCStest ............................... Passed 0.05 sec +64: [04:04:01] Test multithreading (Done) +64: [04:04:01] ------------------------------------- +64: *************************************** +64: *************************************** +64: [04:04:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: [04:04:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +133/223 Test #152: FMCStest ............................... Passed 0.26 sec +test 153 + Start 153: molHashCatchTest + +153: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest +153: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash +153: Test timeout computed to be: 1500 +64: [04:04:01] bond with order 0 found on line 7. This is not part of the MDL specification. +64: [04:04:02] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +64: [04:04:02] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +64: [04:04:02] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +64: generating smiles +64: 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 +64: converting back +153: Randomness seeded to: 2089579027 +153: =============================================================================== +153: All tests passed (304 assertions in 9 test cases) +153: +134/223 Test #153: molHashCatchTest ....................... Passed 0.22 sec test 154 Start 154: pyMolHash 154: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap/testMolHash.py" 154: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap 154: Test timeout computed to be: 1500 -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -146: file test5_2.png gave hash 3891642937U not the expected 3073694291U -148: file rxn_test1_4.png gave hash 326223573U not the expected 2471435686U -132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -146: file test5_3.png gave hash 442326768U not the expected 1865192682U -146: Done -146: ----------------- Test 6 (atom labels) -134: [07:34:58] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -134: [07:34:58] UFFTYPER: Unrecognized atom type: N_5 (2) -134: [07:34:58] UFFTYPER: Unrecognized atom type: N_5 (3) -134: [07:34:58] UFFTYPER: Unrecognized atom type: N_5 (2) -134: [07:34:58] UFFTYPER: Unrecognized atom type: N_5 (3) -146: Done -146: ----------------- Test 7 (backgrounds) -148: file rxn_test1_5.png gave hash 1915733777U not the expected 1428782307U -33: F/C=C/Cl -33: [H]/C(F)=C(/[H])Cl -33: F/C=C/Cl -33: F/C=C/Cl -33: C/C(F)=C(/C)Cl -147: file testGithub3226_1.png gave hash 1140467476U not the expected 2350054896U -146: file test7_1.png gave hash 2325902062U not the expected 3033050306U -113/223 Test #116: pyMolDescriptors3D ..................... Passed 0.67 sec +64: check isomorphism +135: [04:04:02] Molecule does not have explicit Hs. Consider calling AddHs() +128: [04:04:02] done +128: [04:04:02] ------------------------------------- +128: [04:04:02] Test MMFF multithreading3 +130: [04:04:02] done +130: [04:04:02] ------------------------------------- +130: [04:04:02] Testing GitHubIssue62. +130: [04:04:02] beta-lactam 39.6387 +130: [04:04:02] cyclopropanone 174.698 +130: [04:04:02] aziridine 337.986 +130: [04:04:02] aziridinone 115.248 +130: [04:04:02] isobutene 2.48217 +130: [04:04:02] acetone 1.91788 +130: [04:04:02] cyclopentanone 10.1648 +130: [04:04:02] cyclopropene 99.4921 +130: [04:04:02] cyclobutene 41.0156 +130: [04:04:02] cyclopropane 267.236 +130: [04:04:02] gamma-lactam 15.7471 +130: [04:04:03] trans-2,3-diphenylcyclopropan-1-one 203.398 +130: [04:04:03] cis-2,3-diphenylcyclopropan-1-one 206.852 +138: 7055002819 +130: [04:04:03] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +130: [04:04:03] cyclopropylidencyclobutane 218.879 +135: [04:04:03] Molecule does not have explicit Hs. Consider calling AddHs() +130: [04:04:03] diphenylmethylidencyclobutane 79.6139 +130: [04:04:03] done +130: [04:04:03] ------------------------------------- +130: [04:04:03] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +130: [04:04:03] done +130: [04:04:03] ------------------------------------- +130: [04:04:03] Test square planar complexes +130: [04:04:03] done +130: [04:04:03] ------------------------------------- +130: [04:04:03] Test octahedral complexes +130: [04:04:03] done +135/223 Test #130: testUFFForceFieldHelpers ............... Passed 10.74 sec test 155 Start 155: testMMPA 155: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/testMMPA 155: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA 155: Test timeout computed to be: 1500 -134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 1 -147: file testGithub3226_2.png gave hash 1788850357U not the expected 606206725U -146: file test7_2.png gave hash 3963123595U not the expected 3476380724U -146: Done -146: ----------------- Test8: PrepareMolDrawing -132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -146: Done -146: ----------------- Test multi-threaded drawing -146: reading molecules -134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 1 -130: processing -130: launch :0 -130: launch :1 -130: launch :2 -130: launch :3 -114/223 Test #122: pyTestGenerator ........................ Passed 0.60 sec -test 156 - Start 156: pyMMPA - -156: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/Wrap/testMMPA.py" -156: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap -156: Test timeout computed to be: 1500 -130: [07:34:58] Rep: 0 Mol:2 -130: [07:34:58] Rep: [07:34:58] Rep: 00 Mol:3 -130: Mol:1 -130: [07:34:58] Rep: 0 Mol:5 -153: Randomness seeded to: 2552094542 -153: =============================================================================== -153: All tests passed (304 assertions in 9 test cases) -153: -148: file rxn_test1_6.png gave hash 793678174U not the expected 483353696U -147: file testGithub3226_3.png gave hash 2180602679U not the expected 2282880418U -115/223 Test #153: molHashCatchTest ....................... Passed 0.09 sec -test 157 - Start 157: testRascalMCES - -157: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES -157: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES -157: Test timeout computed to be: 1500 -130: [07:34:58] Rep: 0 Mol:0 -130: [07:34:58] Rep: 0 Mol:9 -147: file testPNGMetadata_1.png gave hash 3955478692U not the expected 2423299691U -132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 1 -135: .[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -116/223 Test #33: graphmolMolOpsTest ..................... Passed 1.25 sec -test 158 - Start 158: testRascalCluster - -158: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster -158: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES -158: Test timeout computed to be: 1500 -130: [07:34:58] Rep: 0 Mol:13 -130: [07:34:58] Rep: 0 Mol:4 155: 155: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -155: Time elapsed 0.003918 seconds +155: Time elapsed 0.021443 seconds 155: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 155: 1: NOREF. Reference data NOT LISTED in test case. 155: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -22284,95 +23134,37 @@ 155: 4: NOREF. Reference data NOT LISTED in test case. 155: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 155: 5: NOREF. Reference data NOT LISTED in test case. -146: generating reference drawings 155: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 155: 6: NOREF. Reference data NOT LISTED in test case. 155: 7: res= NULL,C[C:2](C(=O)N[*:1])[NH+]1CCCC1.Cc1ccccc1[*:1] 155: 7: NOREF. Reference data NOT LISTED in test case. 155: 8: res= O=C(N[*:3])[*:1],C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1[*:3] 155: 8: NOREF. Reference data NOT LISTED in test case. -130: [07:34:58] Rep: 0 Mol:7 -130: [07:34:58] Rep: 0 Mol:6 155: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 155: 9: NOREF. Reference data NOT LISTED in test case. -132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 155: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 155: 10: NOREF. Reference data NOT LISTED in test case. -130: [07:34:58] Rep: 0 Mol:11 -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 155: 11: NOREF. Reference data NOT LISTED in test case. -132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 155: 12: NOREF. Reference data NOT LISTED in test case. -132: .[07:34:58] UFFTYPER: Unrecognized hybridization for atom: 0 -132: [07:34:58] UFFTYPER: Unrecognized atom type: Cu+1 (0) 155: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 155: 13: NOREF. Reference data NOT LISTED in test case. -132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: file rxn_test1_7.png gave hash 1232578493U not the expected 528963379U -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 155: 14: NOREF. Reference data NOT LISTED in test case. -132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 155: 15: NOREF. Reference data NOT LISTED in test case. -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 155: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] 155: 16: NOREF. Reference data NOT LISTED in test case. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 17: res= Cc1ccccc1NC(=O)[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] 155: 17: NOREF. Reference data NOT LISTED in test case. -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 155: 18: NOREF. Reference data NOT LISTED in test case. -132: [07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: ..[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -130: [07:34:58] Rep: 0 Mol:17 -132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: file rxn_test1_7.svg gave hash 798375802U not the expected 1881564163U -148: Done -148: ----------------- Test 2: some examples that caused problems in testing -130: [07:34:58] Rep: 0 Mol:15 -132: .[07:34:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -132: .[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -130: [07:34:58] Rep: 0 Mol:10 -132: ..[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -108: =>start test MORSE -108: =>read file -108: [07:34:58] test on : 365 molecules done -130: [07:34:58] Rep: 0 Mol:19 -130: [07:34:58] Rep: 0 Mol:23 -130: [07:34:58] Rep: 0 Mol:27 -130: [07:34:58] Rep: 0 Mol:8 -117/223 Test #108: testMORSE .............................. Passed 0.93 sec -test 159 - Start 159: pyMolDraw2D - -159: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" -159: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap -159: Test timeout computed to be: 1500 -125: ....... -125: ---------------------------------------------------------------------- -125: Ran 7 tests in 0.102s -125: -125: OK 155: 155: --- UNMATCHED Reference RESULTS: --- 155: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 155: ----------------------------------- -155: Time elapsed 0.004986 seconds +155: Time elapsed 0.011727 seconds 155: 155: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 155: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O @@ -22383,12 +23175,17 @@ 155: 3: PASSED. matchedRefRes = 6 155: 4: O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OC[*:2] 155: 4: PASSED. matchedRefRes = 13 +128: [04:04:04] done +128: [04:04:04] ------------------------------------- +128: [04:04:04] Testing github 162: Incorrect SMILES after MMFF parameterization . +128: [04:04:04] done +128: [04:04:04] ------------------------------------- +128: [04:04:04] Testing github 224: crash during MMFF parameterization . +128: [04:04:04] done +128: [04:04:04] ------------------------------------- +128: [04:04:04] Testing github6728: crash due to missing stretch-bend params. 155: 5: O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].O[*:2] 155: 5: PASSED. matchedRefRes = 12 -130: [07:34:58] Rep: 0 Mol:12 -130: [07:34:58] Rep: 0 Mol:31 -148: file rxn_test2_1.png gave hash 160703765U not the expected 399415052U -147: file testPNGMetadata_2.png gave hash 1862211480U not the expected 2803353117U 155: 6: NULL, Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] 155: 6: PASSED. matchedRefRes = 10 155: 7: O=C(N[*:1])[*:2], Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].OCC[*:1] @@ -22399,8 +23196,13 @@ 155: 9: NOREF. Reference data NOT LISTED in test case.O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 155: 10: NULL, Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 155: 10: PASSED. matchedRefRes = 3 -130: [07:34:58] Rep: 0 Mol:16 -132: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() +136/223 Test #128: testMMFFForceFieldHelpers .............. Passed 11.75 sec +test 156 + Start 156: pyMMPA + +156: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/Wrap/testMMPA.py" +156: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap +156: Test timeout computed to be: 1500 155: 11: C([*:1])[*:2], Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 155: 11: NOREF. Reference data NOT LISTED in test case.C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] 155: 12: C(C[*:2])[*:1], Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].O[*:2] @@ -22411,23 +23213,6 @@ 155: 14: PASSED. matchedRefRes = 11 155: 15: NULL, Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 155: 15: PASSED. matchedRefRes = 2 -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -130: [07:34:58] Rep: 0 Mol:20 -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: 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 -141: .[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -130: [07:34:58] Rep: 0 Mol:21 -130: [07:34:58] Rep: 0 Mol:24 -135: ..[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -130: [07:34:58] Rep: 0 Mol:14 155: 155: --- UNMATCHED Reference RESULTS: --- 155: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] @@ -22437,15 +23222,13 @@ 155: ----------------------------------- 155: 155: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -155: Time elapsed 0.005898 seconds +155: Time elapsed 0.012323 seconds 155: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 155: 1: PASSED. matchedRefRes = 4 155: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] 155: 2: PASSED. matchedRefRes = 1 155: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2] 155: 3: PASSED. matchedRefRes = 6 -130: [07:34:58] Rep: 0 Mol:25 -130: [07:34:58] Rep: 0 Mol:28 155: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2] 155: 4: PASSED. matchedRefRes = 13 155: 5: res= O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].O[*:2] @@ -22458,8 +23241,6 @@ 155: 8: NOREF. Reference data NOT LISTED in test case. 155: 9: res= O=C(NCC[*:1])[*:2],Cc1c([*:2])[n+](=O)c2ccccc2n1[O-].O[*:1] 155: 9: NOREF. Reference data NOT LISTED in test case. -148: file rxn_test2_2_1.png gave hash 4057570363U not the expected 1215378243U -130: [07:34:58] Rep: 0 Mol:18 155: 10: res= NULL,Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OCC[*:1] 155: 10: PASSED. matchedRefRes = 3 155: 11: res= C([*:1])[*:2],Cc1c(C(=O)N[*:2])[n+](=O)c2ccccc2n1[O-].OC[*:1] @@ -22472,7 +23253,6 @@ 155: 14: PASSED. matchedRefRes = 11 155: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 155: 15: PASSED. matchedRefRes = 2 -141: .[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 155: --- UNMATCHED Reference RESULTS: --- 155: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] @@ -22482,38 +23262,26 @@ 155: ----------------------------------- 155: 155: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -155: Time elapsed 0.000893 seconds +155: Time elapsed 0.001008 seconds 155: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 155: 1: PASSED. matchedRefRes = 2 155: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] 155: 2: PASSED. matchedRefRes = 3 -148: 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 155: 3: res= C([*:1])([*:2])[*:3],C1CN1[*:3].C[*:1].O=C[*:2] 155: 3: NOREF. Reference data NOT LISTED in test case. -135: .[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 4: res= C1CN1C([*:1])[*:2],C[*:1].O=C[*:2] 155: 4: PASSED. matchedRefRes = 4 155: 5: res= NULL,C1CN1[*:1].CC(C=O)[*:1] 155: 5: PASSED. matchedRefRes = 5 -130: [07:34:58] Rep: 0 Mol:22 155: 6: res= CC([*:1])[*:2],C1CN1[*:2].O=C[*:1] 155: 6: NOREF. Reference data NOT LISTED in test case. 155: 7: res= NULL,CC(N1CC1)[*:1].O=C[*:1] 155: 7: PASSED. matchedRefRes = 7 -118/223 Test #125: pyPartialCharges ....................... Passed 0.66 sec -test 160 - Start 160: testCIPLabeler - -160: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler -160: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler -160: Test timeout computed to be: 1500 -132: ... -132: ---------------------------------------------------------------------- -132: Ran 18 tests in 0.159s -132: -132: OK -130: [07:34:58] Rep: 0 Mol:29 -130: [07:34:58] Rep: 0 Mol:26 +154: ... +154: ---------------------------------------------------------------------- +154: Ran 3 tests in 0.068s +154: +154: OK 155: 155: --- UNMATCHED Reference RESULTS: --- 155: 1: CC(N1CC1)C(=O),Case1-SIMPLE,C([*:1])([*:2])[*:3],C1CN1[*:2].C[*:1].O=C[*:3] @@ -22521,7 +23289,7 @@ 155: ----------------------------------- 155: 155: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -155: Time elapsed 0.003744 seconds +155: Time elapsed 0.020691 seconds 155: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 155: 1: NOREF. Reference data NOT LISTED in test case. 155: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -22530,9 +23298,6 @@ 155: 3: NOREF. Reference data NOT LISTED in test case. 155: 4: res= O=C(Nc1ccccc1[*:1])[C:0]([NH+]1CCCC1)[*:2],C[*:1].C[*:2] 155: 4: NOREF. Reference data NOT LISTED in test case. -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: file rxn_test2_2_2.png gave hash 362458924U not the expected 3645141778U 155: 5: res= O=C(Nc1ccccc1[*:1])[C:0]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].C[*:2] 155: 5: NOREF. Reference data NOT LISTED in test case. 155: 6: res= C[C:0](C(=O)Nc1ccccc1[*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1] @@ -22543,25 +23308,14 @@ 155: 8: NOREF. Reference data NOT LISTED in test case. 155: 9: res= O=C(N[*:2])[C:0]([NH+]1CCCC1)[*:1],C[*:1].Cc1ccccc1[*:2] 155: 9: NOREF. Reference data NOT LISTED in test case. -147: file testGithub3369_1.svg gave hash 1012801087U not the expected 3091976328U 155: 10: res= O=C(N[*:3])[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.C[*:1].Cc1ccccc1[*:3] 155: 10: NOREF. Reference data NOT LISTED in test case. -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -148: 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 -148: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl -148: 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 155: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 155: 11: NOREF. Reference data NOT LISTED in test case. 155: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 155: 12: NOREF. Reference data NOT LISTED in test case. 155: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] 155: 13: NOREF. Reference data NOT LISTED in test case. -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 155: 14: NOREF. Reference data NOT LISTED in test case. 155: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] @@ -22572,50 +23326,33 @@ 155: 17: NOREF. Reference data NOT LISTED in test case. 155: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 155: 18: NOREF. Reference data NOT LISTED in test case. -148: file rxn_test2_2_3.png gave hash 1657316579U not the expected 551946805U -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 155: --- UNMATCHED Reference RESULTS: --- 155: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 155: ----------------------------------- 155: 155: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -155: Time elapsed 0.003990 seconds +155: Time elapsed 0.016700 seconds 155: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 155: 1: NOREF. Reference data NOT LISTED in test case. -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 155: 2: NOREF. Reference data NOT LISTED in test case. -130: [07:34:58] Rep: 0 Mol:30 -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 155: 3: NOREF. Reference data NOT LISTED in test case. -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1 155: 4: NOREF. Reference data NOT LISTED in test case. 155: 5: res= O=C(O[*:1])C([*:2])[*:3],O[*:2].c1ccc(C[*:1])cc1.c1ccc([*:3])cc1 155: 5: NOREF. Reference data NOT LISTED in test case. -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 6: res= O=C(O[*:1])C(O)[*:2],c1ccc(C[*:1])cc1.c1ccc([*:2])cc1 155: 6: NOREF. Reference data NOT LISTED in test case. 155: 7: res= NULL,O=C(OC[*:1])C(O)c1ccccc1.c1ccc([*:1])cc1 155: 7: NOREF. Reference data NOT LISTED in test case. -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 8: res= O=C(OC[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc([*:2])cc1 155: 8: NOREF. Reference data NOT LISTED in test case. 155: 9: res= O=C(OC[*:2])C(c1ccccc1)[*:1],O[*:1].c1ccc([*:2])cc1 155: 9: NOREF. Reference data NOT LISTED in test case. -148: 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 155: 10: res= O=C(OC[*:2])C([*:1])[*:3],O[*:1].c1ccc([*:2])cc1.c1ccc([*:3])cc1 155: 10: NOREF. Reference data NOT LISTED in test case. -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 155: 11: NOREF. Reference data NOT LISTED in test case. 155: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] @@ -22630,841 +23367,837 @@ 155: 16: NOREF. Reference data NOT LISTED in test case. 155: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 155: 17: NOREF. Reference data NOT LISTED in test case. -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 155: 18: NOREF. Reference data NOT LISTED in test case. -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() 155: 155: --- ALL PASSED --- 155: ----------------------------------- 155: 5 TEST CASES FAILED -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -119/223 Test #155: testMMPA ............................... Passed 0.16 sec +137/223 Test #155: testMMPA ............................... Passed 0.46 sec +test 157 + Start 157: testRascalMCES + +157: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES +157: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES +157: Test timeout computed to be: 1500 +133: building molecules +133: generating reference data +138/223 Test #154: pyMolHash .............................. Passed 2.53 sec +test 158 + Start 158: testRascalCluster + +158: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster +158: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES +158: Test timeout computed to be: 1500 +106: =>start test GETAWAY custom +106: [04:04:05] test on : 365 molecules done +139/223 Test #106: testRDFcustom .......................... Passed 16.96 sec +test 159 + Start 159: pyMolDraw2D + +159: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" +159: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RascalMCES/Wrap +159: Test timeout computed to be: 1500 +150: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +150: Time elapsed 0.000 seconds +150: +150: test32() +150: 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 +150: Time elapsed 0.114 seconds +150: +150: test190() +150: 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 +150: Time elapsed 0.016 seconds +150: +150: test3() +150: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds +150: Time elapsed 0.027 seconds +150: +150: testSimpleFast() +150: 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 +150: Time elapsed 0.484 seconds +150: +150: testSimple() +150: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +150: Time elapsed 0.333 seconds +150: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +150: Time elapsed 1.214 seconds +150: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +150: Time elapsed 0.414 seconds +150: +150: testSegFault() +150: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +150: Time elapsed 0.017 seconds +150: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +150: Time elapsed 0.029 seconds +150: 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 +150: Time elapsed 0.029 seconds +150: +150: testThreshold() +150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +150: Time elapsed 0.000 seconds +150: +150: testRing1() +150: 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 +150: Time elapsed 0.541 seconds +150: 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 +150: Time elapsed 0.774 seconds +150: 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 +150: Time elapsed 0.940 seconds +150: +150: testAtomCompareIsotopes() +150: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds +150: Time elapsed 0.000 seconds +150: +150: testAtomCompareAnyAtom() +150: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +150: Time elapsed 0.000 seconds +150: +150: testAtomCompareAnyAtom() +150: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +150: Time elapsed 0.000 seconds +150: +150: testAtomCompareAnyAtom() +150: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds +150: Time elapsed 0.000 seconds +150: +150: testAtomCompareAnyAtom() +150: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds +150: Time elapsed 0.000 seconds +150: +150: testJnk1LigandsDistance() +150: 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 +150: Time elapsed 0.009 seconds +150: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds +150: Time elapsed 0.001 seconds +150: +150: test18() +150: 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 +150: 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 +150: Time elapsed 0.008 seconds +150: +150: test504() +150: 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 +150: 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 +150: Time elapsed 0.108 seconds +150: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +150: Time elapsed 0.001 seconds +150: 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 +150: Time elapsed 0.033 seconds +150: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds +150: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0011 seconds. bond[0]=6 +150: STATISTICS: +150: Total Growing Steps = 1, MCS found on 1 step, for 0.0011 seconds +150: Initial Seeds = 1, Mismatched 0 +150: Inspected Seeds = 2 +150: Rejected by BestSize = 0 +150: IndividualBondExcluded = 0 +150: MatchCheck Seeds = 2 +150: MatchCalls = 2 +150: MatchFound = 1 +150: fastMatchCalls = 1 +150: fastMatchFound = 0 +150: slowMatchCalls = 2 +150: slowMatchFound = 1 +150: DupCacheFound = 0 0 matched, 0 mismatched +150: HashCache size = 1 keys +150: HashCache size = 1 entries +150: FindHashInCache = 2 +150: HashFoundInCache= 0 +150: ExactMatchCalls = 0 +150: ExactMatchFound = 0 +150: Time elapsed 0.001 seconds +150: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 +150: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 +150: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 +150: res sub = 1 size=3 +150: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +150: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 +150: res sub = 1 size=3 +150: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +150: test target = CC[C@H](F)Cl query = CCC useChirality = 0 +150: res sub = 1 size=3 +150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +150: test target = CC[C@H](F)Cl query = CCC useChirality = 1 +150: res sub = 1 size=3 +150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +150: test target = CCC(F)Cl query = CC useChirality = 0 +150: res sub = 1 size=2 +150: MCS: [#6]-[#6] 2 atoms, 1 bonds +150: test target = CCC(F)Cl query = CC useChirality = 1 +150: res sub = 1 size=2 +150: MCS: [#6]-[#6] 2 atoms, 1 bonds +150: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 +150: res sub = 1 size=4 +150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +150: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 +150: res sub = 1 size=4 +150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +150: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 +150: res sub = 1 size=4 +150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +150: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 +150: res sub = 1 size=4 +150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +150: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 +150: res sub = 0 size=0 +150: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +150: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 +150: res sub = 0 size=0 +150: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +150: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 +150: res sub = 1 size=4 +150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +150: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 +150: res sub = 1 size=4 +150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +150: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 +150: res sub = 1 size=4 +150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +150: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 +150: res sub = 1 size=4 +150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +150: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 +150: res sub = 1 size=4 +150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +150: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 +150: res sub = 0 size=0 +150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +150: test target = OC(F)CCl query = OC(F)C useChirality = 0 +150: res sub = 1 size=4 +150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +150: test target = OC(F)CCl query = OC(F)C useChirality = 1 +150: res sub = 1 size=4 +150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +150: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 +150: res sub = 1 size=4 +150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +150: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 +150: res sub = 0 size=0 +150: MCS: [#9] 1 atoms, 0 bonds +150: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 +150: res sub = 1 size=4 +150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +150: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 +150: res sub = 0 size=0 +150: MCS: [#9] 1 atoms, 0 bonds +150: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 +150: res sub = 1 size=3 +150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +150: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 +150: res sub = 1 size=3 +150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +150: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 +150: res sub = 1 size=3 +150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +150: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 +150: res sub = 1 size=3 +150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +150: +150: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> +150: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 +150: res sub = 1 size=3 +150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +150: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 +150: res sub = 1 size=3 +150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +150: done +147: file testHandDrawn-5a.svg gave hash 3172919116U not the expected 3628607349U +147: [04:04:05] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [04:04:05] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +64: [04:04:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +64: [04:04:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +64: [04:04:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +64: [04:04:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +64: [04:04:05] deprecated group abbreviation ignored on line 24 +64: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +64: [04:04:05] +64: +64: **** +64: Post-condition Violation +64: Element 'Mv' not found +64: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +64: Failed Expression: anum > -1 +64: **** +64: +147: file testHandDrawn-5b.svg gave hash 3290430369U not the expected 2522138089U +147: [04:04:05] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [04:04:05] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +147: file testHandDrawn-5.png gave hash 2408781090U not the expected 3439548169U +147: file testBrackets-5a.svg gave hash 4023768529U not the expected 3061667963U +147: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U +147: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U +147: file testPositionVariation-1b.svg gave hash 823876785U not the expected 174339626U +138: 2162693264 +138: =============================================================================== +138: All tests passed (73 assertions in 3 test cases) +138: +140/223 Test #138: molAlignCatchTest ...................... Passed 11.15 sec +test 160 + Start 160: testCIPLabeler + +160: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler +160: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler +160: Test timeout computed to be: 1500 +160: Randomness seeded to: 3929786649 +160: [04:04:06] non kekulizable aromatic bond being treated as bond order 1 +160: [04:04:06] non kekulizable aromatic bond being treated as bond order 1 +160: [04:04:06] non kekulizable aromatic bond being treated as bond order 1 +160: [04:04:06] non kekulizable aromatic bond being treated as bond order 1 +160: [04:04:06] non kekulizable aromatic bond being treated as bond order 1 +160: [04:04:06] non kekulizable aromatic bond being treated as bond order 1 +147: [04:04:06] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U +160: =============================================================================== +160: All tests passed (5977 assertions in 13 test cases) +160: +141/223 Test #160: testCIPLabeler ......................... Passed 0.55 sec test 161 Start 161: pyCIPLabelsWrapTest 161: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" 161: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 161: Test timeout computed to be: 1500 -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: ..[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: .[07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: .[07:34:58] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -141: [07:34:58] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -141: ... -141: ---------------------------------------------------------------------- -141: Ran 9 tests in 0.092s -141: -141: OK -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -146: processing -146: launch :0 -128: processing -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -148: file rxn_test2_2_4.png gave hash 2796626100U not the expected 4234617566U -146: launch :1 -146: launch :2 -146: launch :3 -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -128: [07:34:58] [07:34:58] [07:34:58] Rep: 0Rep: [07:34:58] Rep: 0Rep: 0 Mol: Mol: Mol:0 -128: 1 -128: 0 Mol:3 -128: 2 -128: [07:34:58] Rep: 0 Mol:5 -148: Done -148: ----------------- Test 3: test reactant highlighting -147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -128: [07:34:58] Rep: 0 Mol:9 -128: [07:34:58] Rep: 0 Mol:4 -147: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U -147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -120/223 Test #132: pyForceFieldHelpers .................... Passed 0.63 sec +147: file testGithub4238_1.png gave hash 1562907664U not the expected 3410617836U +147: file testGithub4323_1.png gave hash 3600756148U not the expected 3723958844U +161: ... +161: ---------------------------------------------------------------------- +161: Ran 3 tests in 0.039s +161: +161: OK +147: file testGithub4323_3.png gave hash 1951856443U not the expected 2185913679U +26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +147: [04:04:08] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +142/223 Test #161: pyCIPLabelsWrapTest .................... Passed 1.42 sec test 162 Start 162: pyCIPLabelsValidation 162: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 162: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 162: Test timeout computed to be: 1500 -128: [07:34:58] Rep: 0 Mol:13 -134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 5 -128: [07:34:58] Rep: 0 Mol:8 -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -160: Randomness seeded to: 2977283498 -160: [07:34:58] non kekulizable aromatic bond being treated as bond order 1 -160: [07:34:58] non kekulizable aromatic bond being treated as bond order 1 -160: [07:34:58] non kekulizable aromatic bond being treated as bond order 1 -160: [07:34:58] non kekulizable aromatic bond being treated as bond order 1 -160: [07:34:58] non kekulizable aromatic bond being treated as bond order 1 -160: [07:34:58] non kekulizable aromatic bond being treated as bond order 1 -143: . -143: ---------------------------------------------------------------------- -143: Ran 1 test in 0.082s -143: -143: OK -143: Testing Shape Helpers wrapper -128: [07:34:58] Rep: 0 Mol:17 -147: file testHandDrawn-1.png gave hash 811421521U not the expected 698316547U -128: [07:34:58] Rep: 0 Mol:6 -134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 5 -128: [07:34:58] Rep: 0 Mol:12 -97: .............[07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -128: [07:34:58] Rep: 0 Mol:10 -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -128: [07:34:58] Rep: 0 Mol:7 -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -128: [07:34:58] Rep: 0 Mol:16 -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -128: [07:34:58] Rep: 0 Mol:11 -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -148: file rxn_test3_1.png gave hash 3699939964U not the expected 4176857511U -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -128: [07:34:58] Rep: 0 Mol:15 -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -128: [07:34:58] Rep: 0 Mol:19 -128: [07:34:58] Rep: 0 Mol:23 -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -128: [07:34:58] Rep: 0 Mol:27 -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 5 -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -97: [07:34:58] SMILES Parse Error: syntax error while parsing: --- -97: [07:34:58] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -97: [07:34:58] dasfsadf -128: [07:34:58] Rep: 0 Mol:21 -128: [07:34:58] Rep: 0 Mol:31 -148: file rxn_test3_1.svg gave hash 1959543526U not the expected 2165658826U -128: [07:34:58] Rep: 0 Mol:20 -148: Done -148: ----------------- Test 4: some examples from SMARTS in testing -148: draw! -145: . -145: ---------------------------------------------------------------------- -145: Ran 1 test in 0.011s -145: -145: OK -128: [07:34:58] Rep: 0 Mol:25 -128: [07:34:58] Rep: 0 Mol:24 -128: [07:34:58] Rep: 0 Mol:29 -128: [07:34:58] Rep: 0 Mol:28 -147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -121/223 Test #143: pyShapeHelpers ......................... Passed 0.48 sec +26: All 191 tests passed +135: [04:04:08] Molecule does not have explicit Hs. Consider calling AddHs() +26: +26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +117: [04:04:08] done +117: [04:04:08] ------------------------------------- +117: [04:04:08] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +117: [04:04:08] done +117: [04:04:08] ------------------------------------- +117: [04:04:08] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +117: [04:04:08] done +117: [04:04:08] ------------------------------------- +117: [04:04:08] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +117: [04:04:08] done +117: [04:04:08] ------------------------------------- +117: [04:04:08] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +117: [04:04:08] done +117: [04:04:08] ------------------------------------- +117: [04:04:08] Test unfolded version of RDKFP +117: [04:04:08] ------------------------------------- +117: [04:04:08] Test bitinfo of RDKFP +117: 562: [ 2 ], +117: 709: [ 0 1 ], +117: 1118: [ 0 1 2 ], +117: 1183: [ 1 2 ], +117: 1233: [ 0 1 2 ], +117: 1308: [ 0 ], [ 1 ], +117: 1339: [ 2 ], +117: 1728: [ 1 2 ], +117: 1772: [ 0 ], [ 1 ], +117: 1813: [ 0 1 ], +117: ------------ +117: [04:04:08] ------------------------------------- +117: [04:04:08] Single atoms setting radius 1 bits in Morgan fingerprints +117: [04:04:08] done +117: [04:04:08] ------------------------------------- +117: [04:04:08] Github #879: Pattern fingerprint should set bits for single-atom fragments. +117: [04:04:08] done +117: [04:04:08] ------------------------------------- +117: [04:04:08] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +117: [04:04:08] done +117: [04:04:08] ------------------------------------- +117: [04:04:08] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +117: [04:04:08] done +117: [04:04:08] ------------------------------------- +117: [04:04:08] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +117: [04:04:08] done +117: [04:04:08] ------------------------------------- +117: [04:04:08] Github #2115: BitInfo not complete for RDKFingerprint +117: [04:04:08] done +117: [04:04:08] ------------------------------------- +117: [04:04:08] Github #3723: Fingerprint crash for mols with Zero order bonds +117: [04:04:08] done +143/223 Test #117: testFingerprints ....................... Passed 18.81 sec test 163 Start 163: deprotectTest 163: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 163: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect 163: Test timeout computed to be: 1500 -128: [07:34:58] Rep: 0 Mol:14 -149: ...[07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -149: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -122/223 Test #141: pyChemicalFeatures ..................... Passed 0.56 sec +137: *********************************************************** +137: Testing O3AAlign +137: --------------------------------- +137: testMMFFO3A +137: +137: --------------------------------- +137: testMMFFO3A with pre-computed dmat and MolHistogram +137: +137: --------------------------------- +137: testMMFFO3A with constraints +137: +137: --------------------------------- +137: testMMFFO3A with variable weight constraints followed by local-only optimization +137: +137: --------------------------------- +137: testCrippenO3A +137: +137: --------------------------------- +137: testCrippenO3A with pre-computed dmat and MolHistogram +137: +137: --------------------------------- +137: testCrippenO3A with constraints +137: +137: --------------------------------- +137: testCrippenO3A with variable weight constraints followed by local-only optimization +137: +137: --------------------------------- +137: testMMFFO3A multithreading +137: +137: generating reference data +163: Randomness seeded to: 1801123663 +163: =============================================================================== +163: All tests passed (111 assertions in 3 test cases) +163: +144/223 Test #163: deprotectTest .......................... Passed 0.33 sec test 164 Start 164: pyDeprotect 164: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/rough_test.py" 164: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap 164: Test timeout computed to be: 1500 -128: [07:34:58] Rep: 0 Mol:18 -147: file testHandDrawn-2.svg gave hash 2224670338U not the expected 4132716144U -147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -128: [07:34:58] Rep: 0 Mol:22 -123/223 Test #145: pyMolCatalog ........................... Passed 0.48 sec +135: [04:04:09] Molecule does not have explicit Hs. Consider calling AddHs() +164: ..... +164: ---------------------------------------------------------------------- +164: Ran 5 tests in 0.097s +164: +164: OK +164: Testing tert-butyldimethylsilyl +164: Testing methoxytrityl +164: Testing tetrahydropyranyl +164: Testing methoxymethyl_ether +164: Testing beta-Methoxyethoxymethyl_ether +164: Testing benzyl +164: Testing trimethylsilyl +164: Testing benzoyl +164: Testing pivaloyl +164: Testing triisopropylsilyl +164: Testing acetyl +164: Testing para-methoxybenzyl_ether +164: Testing triphenylmethyl +164: Testing phthaloyl +164: Testing trimethylsilylethoxymethyl +164: Testing para-methoxyphenyl +164: Testing tosyl +164: Testing tert-butyloxycarbonyl +164: Testing trifluoroacetyl +164: Testing benzoyl +164: Testing 9-fluorenylmethyloxycarbonyl +164: Testing benzylamine +164: Testing acetamide +164: Testing carbobenzyloxy +164: Testing Acetal/Ketal +164: Testing tert-butyldimethylsilyl +164: Testing methoxytrityl +164: Testing tetrahydropyranyl +164: Testing methoxymethyl_ether +164: Testing beta-Methoxyethoxymethyl_ether +164: Testing benzyl +164: Testing trimethylsilyl +164: Testing benzoyl +164: Testing pivaloyl +164: Testing triisopropylsilyl +164: Testing acetyl +164: Testing para-methoxybenzyl_ether +164: Testing triphenylmethyl +164: Testing phthaloyl +164: Testing trimethylsilylethoxymethyl +164: Testing para-methoxyphenyl +164: Testing tosyl +164: Testing tert-butyloxycarbonyl +164: Testing trifluoroacetyl +164: Testing benzoyl +164: Testing 9-fluorenylmethyloxycarbonyl +164: Testing benzylamine +164: Testing acetamide +164: Testing carbobenzyloxy +164: Testing Acetal/Ketal +145/223 Test #164: pyDeprotect ............................ Passed 0.95 sec test 165 Start 165: testReducedGraphs 165: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs 165: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs 165: Test timeout computed to be: 1500 -148: file rxn_test4_1.png gave hash 1897728811U not the expected 4187207676U -128: [07:34:58] Rep: 0 Mol:26 -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -147: file testHandDrawn-2.png gave hash 928126416U not the expected 1605553248U -148: file rxn_test4_1.svg gave hash 2683567127U not the expected 3239755313U -148: done -147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -147: file testHandDrawn-3.svg gave hash 633044862U not the expected 4199337510U -147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -128: [07:34:58] Rep: 0 Mol:30 -147: file testHandDrawn-3.png gave hash 2410179907U not the expected 2881952238U -147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -147: file testHandDrawn-4.svg gave hash 2180320567U not the expected 4197407865U -147: [07:34:58] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [07:34:58] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -154: ... -154: ---------------------------------------------------------------------- -154: Ran 3 tests in 0.015s -154: -154: OK +150: [04:04:10] The provided InitialSeed is not an MCS and will be ignored 165: 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, ] 165: 165: 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, ] 165: 165: 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, 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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, 0.3, 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, ] 165: -160: =============================================================================== -160: All tests passed (5977 assertions in 13 test cases) -160: -147: file testHandDrawn-4.png gave hash 1714306199U not the expected 3431655453U -124/223 Test #160: testCIPLabeler ......................... Passed 0.25 sec +165: 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, ] +165: +165: 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, ] +165: +165: 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, ] +165: +146/223 Test #165: testReducedGraphs ...................... Passed 0.11 sec test 166 Start 166: pyReducedGraphs 166: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" 166: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap 166: Test timeout computed to be: 1500 -163: Randomness seeded to: 3508537481 -163: =============================================================================== -163: All tests passed (111 assertions in 3 test cases) -163: -165: 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, ] -165: -125/223 Test #163: deprotectTest .......................... Passed 0.09 sec +135: [04:04:10] Molecule does not have explicit Hs. Consider calling AddHs() +147: file testFlexiCanvas.2a.png gave hash 3809318030U not the expected 3217758043U +147: file testFlexiCanvas.2b.png gave hash 1941040420U not the expected 4070063910U +147: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U +159: ........ +159: ---------------------------------------------------------------------- +159: Ran 8 tests in 5.012s +159: +159: OK +135: [04:04:11] Molecule does not have explicit Hs. Consider calling AddHs() +147: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U +147: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U +147: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U +147: file testGithub4764.sz1.png gave hash 1936053216U not the expected 98827714U +147: file testGithub4764.sz2.png gave hash 518440428U not the expected 89252465U +156: ......... +156: ---------------------------------------------------------------------- +156: Ran 9 tests in 6.321s +156: +156: OK +147/223 Test #159: pyMolDraw2D ............................ Passed 6.32 sec test 167 Start 167: trajectoryTest 167: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 167: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory 167: Test timeout computed to be: 1500 -165: 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, ] -165: -165: 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, ] -165: -135: [07:34:58] Molecule does not have explicit Hs. Consider calling AddHs() -126/223 Test #165: testReducedGraphs ...................... Passed 0.08 sec +147: file testGithub4764.sz3.png gave hash 1437648833U not the expected 148503574U +147: file testGithub_5061.svg gave hash 4026821599U not the expected 83338095U +148/223 Test #156: pyMMPA ................................. Passed 7.71 sec test 168 Start 168: substructLibraryTest 168: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 168: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary 168: Test timeout computed to be: 1500 -134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 6 -149: ..........[07:34:58] -149: -149: **** -149: Pre-condition Violation -149: molecule must not be None -149: Violation occurred on line 432 in file ./Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp -149: Failed Expression: m -149: **** -149: -148: file rxn_test4_2.png gave hash 3724924058U not the expected 3490081297U -134: [07:34:58] UFFTYPER: Unrecognized charge state for atom: 6 -127/223 Test #154: pyMolHash .............................. Passed 0.44 sec +147: file github5383_1.svg gave hash 2850811663U not the expected 3666750661U +166: ..... +166: ---------------------------------------------------------------------- +166: Ran 5 tests in 0.062s +166: +166: OK +147: file github5383_2.svg gave hash 1346330069U not the expected 0U +147: file github5383_1.png gave hash 3128184037U not the expected 992803933U +168: [04:04:11] ------------------------------------- +168: [04:04:11] Test1 +147: file acs1996_1.png gave hash 1346742279U not the expected 2957839025U +147: file acs1996_2.png gave hash 806461087U not the expected 2664798808U +147: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U +147: [04:04:12] 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. +147: file bond_highlights_8.svg gave hash 682598716U not the expected 2956924065U +149/223 Test #166: pyReducedGraphs ........................ Passed 1.66 sec test 169 Start 169: substructLibraryCatchTest 169: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 169: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary 169: Test timeout computed to be: 1500 -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -168: [07:34:59] ------------------------------------- -168: [07:34:59] Test1 -134: [07:34:59] UFFTYPER: Unrecognized charge state for atom: 6 -148: file rxn_test4_2.svg gave hash 4278906476U not the expected 4127054729U -148: Done -128/223 Test #148: moldraw2DRxnTest1 ...................... Passed 0.58 sec +135: [04:04:12] Molecule does not have explicit Hs. Consider calling AddHs() +150/223 Test #167: trajectoryTest ......................... Passed 0.88 sec test 170 Start 170: pySubstructLibrary 170: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" 170: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 170: Test timeout computed to be: 1500 -106: =>start test morse custom -106: [07:34:59] test on : 365 molecules done -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -128: [07:34:59] Rep: 20 Mol:3 -128: [07:34:59] Rep: 20 Mol:7 -128: [07:34:59] Rep: 20 Mol:11 -128: [07:34:59] Rep: 20 Mol:15 -128: [07:34:59] Rep: 20 Mol:19 -128: [07:34:59] Rep: 20 Mol:23 -128: [07:34:59] Rep: 20 Mol:27 -128: [07:34:59] Rep: 20 Mol:31 -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -119: [07:34:59] done -119: [07:34:59] ------------------------------------- -119: [07:34:59] Test GitHub Issue #6958 -97: ....... -97: ---------------------------------------------------------------------- -97: Ran 21 tests in 1.125s -97: -97: OK -97: (Five aromatic carbons And (Not any of Five aromatic carbons)) -97: (Five aromatic carbons Or (Not any of Five aromatic carbons)) -97: (Not (Five aromatic carbons And (Not any of Five aromatic carbons))) -97: ******************************************** -97: Testing: PAINS_A 2 -97: ******************************************** -97: Testing: PAINS_B 4 -97: ******************************************** -97: Testing: PAINS_C 8 -97: ******************************************** -97: Testing: PAINS 14 -97: (Not FilterMatcher) -97: Bar -97: Count 1 -97: ******************************************** -97: {'Cl,Br,I'} -97: 1 -97: 2 -97: running -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -129/223 Test #119: testFingerprintGenerators .............. Passed 1.13 sec +168: [04:04:12] done +168: [04:04:12] ------------------------------------- +168: [04:04:12] Test2 +147: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U +147: file github6504_1.svg gave hash 3649936662U not the expected 1429448598U +147: file github6504_2.svg gave hash 106020287U not the expected 2871662880U +147: file github6569_1.svg gave hash 1698514747U not the expected 116573839U +147: file github6569_2.svg gave hash 2778768241U not the expected 2367779037U +147: file lasso_highlights_1.svg gave hash 2411984833U not the expected 689837467U +147: file lasso_highlights_2.svg gave hash 1109702647U not the expected 348394942U +147: file lasso_highlights_3.svg gave hash 2940545227U not the expected 2174136207U +147: file lasso_highlights_4.svg gave hash 3276894790U not the expected 1265047504U +147: file lasso_highlights_5.svg gave hash 2028645321U not the expected 35778943U +147: file lasso_highlights_6.svg gave hash 1732575234U not the expected 1359376880U +135: [04:04:13] Molecule does not have explicit Hs. Consider calling AddHs() +147: file lasso_highlights_7.svg gave hash 1593492996U not the expected 773081917U +168: [04:04:13] done +168: [04:04:13] ------------------------------------- +168: [04:04:13] Test3 (stereo options) +147: file bad_lasso_1.svg gave hash 1431427975U not the expected 1183031575U +147: =============================================================================== +147: All tests passed (6525 assertions in 94 test cases) +147: +151/223 Test #147: moldraw2DTestCatch ..................... Passed 16.03 sec test 171 Start 171: testRGroupDecomp 171: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 171: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 171: Test timeout computed to be: 1500 -128: [07:34:59] Rep: 20 Mol:1 -128: [07:34:59] Rep: 20 Mol:5 -128: [07:34:59] Rep: 20 Mol:9 -128: [07:34:59] Rep: 20 Mol:13 -128: [07:34:59] Rep: 20 Mol:17 -128: [07:34:59] Rep: 20 Mol:21 -128: [07:34:59] Rep: 20 Mol:25 -128: [07:34:59] Rep: 20 Mol:29 -130: [07:34:59] Rep: 100 Mol:0 -130: [07:34:59] Rep: 100 Mol:4 -130: [07:34:59] Rep: 100 Mol:8 -130: [07:34:59] Rep: 100 Mol:12 -130: [07:34:59] Rep: 100 Mol:16 -130: [07:34:59] Rep: 100 Mol:20 -130: [07:34:59] Rep: 100 Mol:24 -130: [07:34:59] Rep: 100 Mol:28 -161: ... -161: ---------------------------------------------------------------------- -161: Ran 3 tests in 0.024s -161: -161: OK -128: [07:34:59] Rep: 20 Mol:0 -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -128: [07:34:59] Rep: 20 Mol:4 -128: [07:34:59] Rep: 20 Mol:8 -128: [07:34:59] Rep: 20 Mol:12 -128: [07:34:59] Rep: 20 Mol:16 -128: [07:34:59] Rep: 20 Mol:20 -128: [07:34:59] Rep: 20 Mol:24 -128: [07:34:59] Rep: 20 Mol:28 -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -149: ..................... -149: ---------------------------------------------------------------------- -149: Ran 34 tests in 0.397s -149: -149: OK -149: json lasso -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -130/223 Test #97: pyFilterCatalog ........................ Passed 1.60 sec +168: [04:04:13] Done (stereo options) +168: [04:04:13] ------------------------------------- +168: [04:04:13] Test4 (trusted smiles) +168: [04:04:13] Done (trusted smiles) +168: [04:04:13] ------------------------------------- +168: [04:04:13] Testing C++ docs +168: [04:04:13] Done (C++ doc tests) +168: [04:04:13] ------------------------------------- +168: [04:04:13] Testing C++ ring query: PatternHolder +168: [04:04:13] Done (C++ ring query tests) +168: [04:04:13] ------------------------------------- +168: [04:04:13] Testing C++ ring query: TautomerPatternHolder +168: [04:04:13] Done (C++ ring query tests) +168: [04:04:13] ------------------------------------- +168: [04:04:13] Add Patterns +169: Randomness seeded to: 3337319383 +169: =============================================================================== +169: All tests passed (171 assertions in 5 test cases) +169: +152/223 Test #169: substructLibraryCatchTest .............. Passed 2.24 sec test 172 Start 172: testRGroupDecompInternals 172: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 172: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 172: Test timeout computed to be: 1500 -128: [07:34:59] Rep: 40 Mol:3 -128: [07:34:59] Rep: 40 Mol:7 -128: [07:34:59] Rep: 40 Mol:11 -131/223 Test #161: pyCIPLabelsWrapTest .................... Passed 0.51 sec +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [04:04:14] WARNING: not removing hydrogen atom with dummy atom neighbors +153/223 Test #172: testRGroupDecompInternals .............. Passed 0.23 sec test 173 Start 173: rgroupCatchTests 173: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 173: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 173: Test timeout computed to be: 1500 -128: [07:34:59] Rep: 40 Mol:15 -128: [07:34:59] Rep: 40 Mol:19 -128: [07:34:59] Rep: 40 Mol:23 -128: [07:34:59] Rep: 40 Mol:27 -128: [07:34:59] Rep: 40 Mol:31 -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -128: [07:34:59] Rep: 20 Mol:2 -168: [07:34:59] done -128: [07:34:59] Rep: 20 Mol:6 -128: [07:34:59] Rep: 20 Mol:10 -128: [07:34:59] Rep: 20 Mol:14 -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -128: [07:34:59] Rep: 20 Mol:18 -128: [07:34:59] Rep: 20 Mol:22 -128: [07:34:59] Rep: 20 Mol:26 -168: [07:34:59] ------------------------------------- -168: [07:34:59] Test2 -128: [07:34:59] Rep: 20 Mol:30 -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -132/223 Test #149: pyMolDraw2D ............................ Passed 0.91 sec +133: validating reference data +64: [04:04:14] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +64: [04:04:14] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +64: ---------------------------------- +64: ---------------------------------- +64: [04:04:15] +64: +64: **** +64: Pre-condition Violation +64: rlabel out of range for MDL files +64: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp +64: Failed Expression: rlabel >= 0 && rlabel < 100 +64: **** +64: +64: [04:04:15] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +171: [04:04:15] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +171: [04:04:15] WARNING: not removing hydrogen atom with dummy atom neighbors +173: Randomness seeded to: 3193704082 +173: =============================================================================== +173: All tests passed (203 assertions in 13 test cases) +173: +154/223 Test #173: rgroupCatchTests ....................... Passed 1.06 sec test 174 Start 174: pyRGroupDecomposition 174: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 174: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 174: Test timeout computed to be: 1500 -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -130: [07:34:59] Rep: 100 Mol:3 -130: [07:34:59] Rep: 100 Mol:7 -130: [07:34:59] Rep: 100 Mol:11 -130: [07:34:59] Rep: 100 Mol:15 -130: [07:34:59] Rep: 100 Mol:19 -133/223 Test #172: testRGroupDecompInternals .............. Passed 0.10 sec +157: Randomness seeded to: 2785122575 +157: Timed out after 11 seconds. +137: processing +137: launch :0 +137: launch :1 +137: launch :2 +137: launch :3 +135: .[04:04:15] Molecule does not have explicit Hs. Consider calling AddHs() +64: [04:04:16] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +64: [04:04:16] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +64: [04:04:16] Empty atom list: 'M ALS 1 0 F' on line 8. +155/223 Test #64: fileParsersTest1 ....................... Passed 30.38 sec test 175 Start 175: molInterchangeTest1 175: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 175: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 175: Test timeout computed to be: 1500 -130: [07:34:59] Rep: 100 Mol:23 -130: [07:34:59] Rep: 100 Mol:27 -130: [07:34:59] Rep: 100 Mol:31 -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -135: .[07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -166: ..... -166: ---------------------------------------------------------------------- -166: Ran 5 tests in 0.017s -166: -166: OK -175: [07:34:59] test1: basics -175: [07:34:59] done -175: [07:34:59] test2: basic writing +175: [04:04:16] test1: basics +175: [04:04:16] done +175: [04:04:16] test2: basic writing 175: {"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":"2023.09.3","cipRanks":[0,0]}]}]} 175: {"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":"2023.09.3","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 175: {"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":"2023.09.3","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]]}]}]} 175: {"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":"2023.09.3","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]]}]}]} -175: [07:34:59] done -175: [07:34:59] test3: writing conformers +175: [04:04:16] done +175: [04:04:16] test3: writing conformers 175: {"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":[[-1.1987,-0.0452],[-0.3332,0.4555],[0.1659,1.322],[0.5332,-0.0438],[-2.0652,0.4541],[-0.8339,1.3212]]},{"dim":3,"coords":[[0.9553,-0.3743,-0.4679],[-0.3616,-0.131,-0.0794],[-0.5097,1.6255,0.1705],[-0.5778,-0.7919,1.1042],[1.5276,0.1063,0.1627],[-1.0339,-0.4345,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2023.09.3","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} -175: [07:34:59] done -175: [07:34:59] test4: writing properties +175: [04:04:16] done +175: [04:04:16] test4: writing properties 175: {"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":"2023.09.3","cipRanks":[0,0]}]}]} -175: [07:34:59] done -175: [07:34:59] test5: writing partial charges +175: [04:04:16] done +175: [04:04:16] test5: writing partial charges 175: {"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":"2023.09.3","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2023.09.3","values":[0.5,-0.5]}]}]} -175: [07:34:59] testing parse options -175: [07:34:59] done -175: [07:34:59] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +175: [04:04:16] testing parse options +175: [04:04:16] done +175: [04:04:16] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 175: {"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":"2023.09.3","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -175: [07:34:59] done -175: [07:34:59] testing 'either' stereochemistry -175: [07:34:59] done -134/223 Test #175: molInterchangeTest1 .................... Passed 0.07 sec +175: [04:04:16] done +175: [04:04:16] testing 'either' stereochemistry +175: [04:04:16] done +156/223 Test #175: molInterchangeTest1 .................... Passed 0.11 sec test 176 Start 176: molInterchangeCatchTest 176: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 176: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 176: Test timeout computed to be: 1500 -135/223 Test #166: pyReducedGraphs ........................ Passed 0.49 sec +176: Randomness seeded to: 1170364871 +176: [04:04:16] unrecognized bond type 12 set to zero while writing +176: [04:04:16] unrecognized bond type 0 set to zero while writing +176: =============================================================================== +176: All tests passed (117 assertions in 5 test cases) +176: +157/223 Test #176: molInterchangeCatchTest ................ Passed 0.20 sec test 177 Start 177: pyMolInterchange 177: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 177: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 177: Test timeout computed to be: 1500 -176: Randomness seeded to: 2932294546 -128: [07:34:59] Rep: 60 Mol:3 -128: [07:34:59] Rep: 60 Mol:7 -128: [07:34:59] Rep: 60 Mol:11 -128: [07:34:59] Rep: 60 Mol:15 -128: [07:34:59] Rep: 60 Mol:19 -128: [07:34:59] Rep: 60 Mol:23 -128: [07:34:59] Rep: 60 Mol:27 -128: [07:34:59] Rep: 60 Mol:31 -176: [07:34:59] unrecognized bond type 12 set to zero while writing -176: [07:34:59] unrecognized bond type 0 set to zero while writing -176: =============================================================================== -176: All tests passed (117 assertions in 5 test cases) -176: -136/223 Test #176: molInterchangeCatchTest ................ Passed 0.05 sec +84: 0,0 0 +84: 0,1 0 +84: 1,0 0 +84: 1,1 0 +84: 2,0 0 +84: 2,1 0 +158/223 Test #84: testEnumeration ........................ Passed 31.03 sec test 178 Start 178: testSLNParse 178: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 178: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse 178: Test timeout computed to be: 1500 -178: [07:34:59] SLN Parse Error: syntax error while parsing: CH4[I=13] -178: [07:34:59] Failed parsing SLN 'CH4[I=13]' -164: ..... -164: ---------------------------------------------------------------------- -164: Ran 5 tests in 0.049s -164: -164: OK -164: Testing tert-butyldimethylsilyl -164: Testing methoxytrityl -164: Testing tetrahydropyranyl -164: Testing methoxymethyl_ether -164: Testing beta-Methoxyethoxymethyl_ether -164: Testing benzyl -164: Testing trimethylsilyl -164: Testing benzoyl -164: Testing pivaloyl -164: Testing triisopropylsilyl -164: Testing acetyl -164: Testing para-methoxybenzyl_ether -164: Testing triphenylmethyl -164: Testing phthaloyl -164: Testing trimethylsilylethoxymethyl -164: Testing para-methoxyphenyl -164: Testing tosyl -164: Testing tert-butyloxycarbonyl -164: Testing trifluoroacetyl -164: Testing benzoyl -164: Testing 9-fluorenylmethyloxycarbonyl -164: Testing benzylamine -164: Testing acetamide -164: Testing carbobenzyloxy -164: Testing Acetal/Ketal -164: Testing tert-butyldimethylsilyl -164: Testing methoxytrityl -164: Testing tetrahydropyranyl -164: Testing methoxymethyl_ether -164: Testing beta-Methoxyethoxymethyl_ether -164: Testing benzyl -164: Testing trimethylsilyl -164: Testing benzoyl -164: Testing pivaloyl -164: Testing triisopropylsilyl -164: Testing acetyl -164: Testing para-methoxybenzyl_ether -164: Testing triphenylmethyl -164: Testing phthaloyl -164: Testing trimethylsilylethoxymethyl -164: Testing para-methoxyphenyl -164: Testing tosyl -164: Testing tert-butyloxycarbonyl -164: Testing trifluoroacetyl -164: Testing benzoyl -164: Testing 9-fluorenylmethyloxycarbonyl -164: Testing benzylamine -164: Testing acetamide -164: Testing carbobenzyloxy -164: Testing Acetal/Ketal -178: [07:34:59] SLN Parser error: Atom ID 1 appears *after* its ring closure. -178: [07:34:59] SLN Parser error: Ring closure 1 does not have a corresponding opener. -178: [07:34:59] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -178: [07:34:59] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -178: [07:34:59] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -178: [07:34:59] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -178: [07:34:59] SLN Parse Error: syntax error while parsing: CH4 fff -178: [07:34:59] Failed parsing SLN 'CH4 fff' -178: [07:34:59] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -178: [07:34:59] Failed parsing SLN 'C[charge=+1] foo' -128: [07:34:59] Rep: 40 Mol:1 -178: [07:34:59] Query property 'is' ignored on non-query atom -128: [07:34:59] Rep: 40 Mol:5 -178: [07:34:59] Query property 'is' ignored on non-query atom -128: [07:34:59] Rep: 40 Mol:9 -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -173: Randomness seeded to: 3346413248 -173: =============================================================================== -173: All tests passed (203 assertions in 13 test cases) -173: -137/223 Test #178: testSLNParse ........................... Passed 0.05 sec +178: [04:04:18] SLN Parse Error: syntax error while parsing: CH4[I=13] +178: [04:04:18] Failed parsing SLN 'CH4[I=13]' +178: [04:04:18] SLN Parser error: Atom ID 1 appears *after* its ring closure. +178: [04:04:18] SLN Parser error: Ring closure 1 does not have a corresponding opener. +178: [04:04:18] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +178: [04:04:18] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +178: [04:04:18] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +178: [04:04:18] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +178: [04:04:18] SLN Parse Error: syntax error while parsing: CH4 fff +178: [04:04:18] Failed parsing SLN 'CH4 fff' +178: [04:04:18] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +178: [04:04:18] Failed parsing SLN 'C[charge=+1] foo' +178: [04:04:18] Query property 'is' ignored on non-query atom +178: [04:04:18] Query property 'is' ignored on non-query atom +159/223 Test #178: testSLNParse ........................... Passed 0.17 sec test 179 Start 179: pySLNParse 179: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/Wrap/testSLN.py" 179: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap 179: Test timeout computed to be: 1500 -138/223 Test #173: rgroupCatchTests ....................... Passed 0.28 sec +177: .. +177: ---------------------------------------------------------------------- +177: Ran 2 tests in 0.058s +177: +177: OK +160/223 Test #177: pyMolInterchange ....................... Passed 1.66 sec test 180 Start 180: pyGraphMolWrap 180: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rough_test.py" 180: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 180: Test timeout computed to be: 1500 -128: [07:34:59] Rep: 40 Mol:13 -128: [07:34:59] Rep: 40 Mol:17 -128: [07:34:59] Rep: 40 Mol:21 -128: [07:34:59] Rep: 40 Mol:25 -128: [07:34:59] Rep: 40 Mol:29 -139/223 Test #167: trajectoryTest ......................... Passed 0.62 sec +179: .. +179: ---------------------------------------------------------------------- +179: Ran 2 tests in 0.013s +179: +179: OK +161/223 Test #179: pySLNParse ............................. Passed 1.01 sec test 181 Start 181: pyTestConformerWrap 181: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testConformer.py" 181: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 181: Test timeout computed to be: 1500 -140/223 Test #164: pyDeprotect ............................ Passed 0.71 sec +181: ...... +181: ---------------------------------------------------------------------- +181: Ran 6 tests in 0.031s +181: +181: OK +162/223 Test #181: pyTestConformerWrap .................... Passed 1.21 sec test 182 Start 182: pyTestTrajectory 182: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testTrajectory.py" 182: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 182: Test timeout computed to be: 1500 -128: [07:34:59] Rep: 40 Mol:0 -106: =>start test AUTOCORR3D custom -106: [07:34:59] test on : 365 molecules done -169: Randomness seeded to: 1579871511 -169: =============================================================================== -169: All tests passed (171 assertions in 5 test cases) -169: -128: [07:34:59] Rep: 40 Mol:4 -128: [07:34:59] Rep: 40 Mol:8 -128: [07:34:59] Rep: 40 Mol:12 -128: [07:34:59] Rep: 40 Mol:16 -141/223 Test #169: substructLibraryCatchTest .............. Passed 0.65 sec -test 183 - Start 183: pyTestSGroups - -183: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testSGroups.py" -183: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -183: Test timeout computed to be: 1500 -128: [07:34:59] Rep: 40 Mol:2 -128: [07:34:59] Rep: 40 Mol:6 -128: [07:34:59] Rep: 40 Mol:10 -128: [07:34:59] Rep: 40 Mol:20 -128: [07:34:59] Rep: 40 Mol:14 -128: [07:34:59] Rep: 40 Mol:24 -128: [07:34:59] Rep: 40 Mol:18 -128: [07:34:59] Rep: 40 Mol:28 -128: [07:34:59] Rep: 40 Mol:22 -128: [07:34:59] Rep: 40 Mol:26 -128: [07:34:59] Rep: 40 Mol:30 -128: [07:34:59] Rep: 80 Mol:3 -128: [07:34:59] Rep: 80 Mol:7 -128: [07:34:59] Rep: 80 Mol:11 -128: [07:34:59] Rep: 80 Mol:15 -128: [07:34:59] Rep: 80 Mol:19 -128: [07:34:59] Rep: 80 Mol:23 -128: [07:34:59] Rep: 80 Mol:27 -128: [07:34:59] Rep: 80 Mol:31 -168: [07:34:59] done -168: [07:34:59] ------------------------------------- -168: [07:34:59] Test3 (stereo options) -171: [07:34:59] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -135: [07:34:59] Molecule does not have explicit Hs. Consider calling AddHs() -171: [07:34:59] WARNING: not removing hydrogen atom with dummy atom neighbors -130: [07:34:59] Rep: 100 Mol:1 -130: [07:34:59] Rep: 100 Mol:5 -130: [07:34:59] Rep: 100 Mol:9 -130: [07:34:59] Rep: 100 Mol:13 -130: [07:34:59] Rep: 100 Mol:17 -130: [07:34:59] Rep: 100 Mol:21 -130: [07:34:59] Rep: 100 Mol:25 -130: [07:34:59] Rep: 100 Mol:29 -106: =>start test 2 WHIM custom -106: [07:34:59] test on : 365 molecules done -147: file testHandDrawn-5a.svg gave hash 3172919116U not the expected 3628607349U -147: [07:34:59] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [07:34:59] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -168: [07:34:59] Done (stereo options) -168: [07:34:59] ------------------------------------- -168: [07:34:59] Test4 (trusted smiles) -147: file testHandDrawn-5b.svg gave hash 3290430369U not the expected 2522138089U -147: [07:34:59] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [07:34:59] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -128: [07:34:59] Rep: 60 Mol:1 -128: [07:34:59] Rep: 60 Mol:5 -128: [07:34:59] Rep: 60 Mol:9 -128: [07:34:59] Rep: 60 Mol:13 -128: [07:34:59] Rep: 60 Mol:17 -128: [07:34:59] Rep: 60 Mol:21 -128: [07:34:59] Rep: 60 Mol:25 -128: [07:34:59] Rep: 60 Mol:29 -26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -168: [07:34:59] Done (trusted smiles) -168: [07:34:59] ------------------------------------- -168: [07:34:59] Testing C++ docs -168: [07:34:59] Done (C++ doc tests) -168: [07:34:59] ------------------------------------- -168: [07:34:59] Testing C++ ring query: PatternHolder -168: [07:34:59] Done (C++ ring query tests) -168: [07:34:59] ------------------------------------- -168: [07:34:59] Testing C++ ring query: TautomerPatternHolder -168: [07:34:59] Done (C++ ring query tests) -168: [07:34:59] ------------------------------------- -168: [07:34:59] Add Patterns -87: . -87: ---------------------------------------------------------------------- -87: Ran 11 tests in 1.997s -87: -87: OK -87: True -87: == CartesianProductStrategy CartesianProductStrategy -87: 197 out of 300 -87: 0 6 out of 10 -87: 1 3 out of 5 -87: 2 4 out of 6 -87: 198 out of 300 -87: 0 10 out of 10 -87: 1 5 out of 5 -87: 2 6 out of 6 -87: Skipped 10000000 in 0.0670316219329834 seconds -87: Skipped 10000000 in 0.9053530693054199 seconds -87: Skipped 10000000 in 0.6273438930511475 seconds -147: file testHandDrawn-5.png gave hash 2408781090U not the expected 3439548169U -179: .. -179: ---------------------------------------------------------------------- -179: Ran 2 tests in 0.023s -179: -179: OK -147: file testBrackets-5a.svg gave hash 4023768529U not the expected 3061667963U -130: [07:35:00] Rep: 100 Mol:2 -130: [07:35:00] Rep: 100 Mol:6 -130: [07:35:00] Rep: 100 Mol:10 -130: [07:35:00] Rep: 100 Mol:14 -130: [07:35:00] Rep: 100 Mol:18 -130: [07:35:00] Rep: 100 Mol:22 -130: [07:35:00] Rep: 100 Mol:26 -130: [07:35:00] Rep: 100 Mol:30 -147: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U -147: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U -147: file testPositionVariation-1b.svg gave hash 823876785U not the expected 174339626U -128: [07:35:00] Rep: 60 Mol:0 -128: [07:35:00] Rep: 60 Mol:4 -128: [07:35:00] Rep: 60 Mol:8 -177: .. -177: ---------------------------------------------------------------------- -177: Ran 2 tests in 0.034s -177: -177: OK -26: All 191 tests passed -128: [07:35:00] Rep: 60 Mol:12 -128: [07:35:00] Rep: 60 Mol:16 -128: [07:35:00] Rep: 60 Mol:20 -128: [07:35:00] Rep: 60 Mol:24 -128: [07:35:00] Rep: 60 Mol:28 -142/223 Test #179: pySLNParse ............................. Passed 0.55 sec -test 184 - Start 184: pyTestThreads - -184: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testThreads.py" -184: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -184: Test timeout computed to be: 1500 -128: [07:35:00] Rep: 60 Mol:2 -128: [07:35:00] Rep: 60 Mol:6 -128: [07:35:00] Rep: 60 Mol:10 -182: [07:35:00] +151: ........................................[04:04:20] The provided InitialSeed is not an MCS and will be ignored +151: [04:04:20] The provided InitialSeed is not an MCS and will be ignored +151: [04:04:20] The provided InitialSeed is not an MCS and will be ignored +151: .[04:04:20] The provided InitialSeed is not an MCS and will be ignored +151: [04:04:20] The provided InitialSeed is not an MCS and will be ignored +151: [04:04:20] The provided InitialSeed is not an MCS and will be ignored +151: .[04:04:20] The provided InitialSeed is not an MCS and will be ignored +151: [04:04:20] The provided InitialSeed is not an MCS and will be ignored +151: [04:04:20] The provided InitialSeed is not an MCS and will be ignored +151: .[04:04:21] The provided InitialSeed is not an MCS and will be ignored +133: processing +133: launch :0 +133: launch :1 +133: launch :2 +133: launch :3 +151: [04:04:21] The provided InitialSeed is not an MCS and will be ignored +151: [04:04:21] The provided InitialSeed is not an MCS and will be ignored +168: [04:04:21] ------------------------------------- +168: [04:04:21] testing PatternHolder +151: ................. +151: ---------------------------------------------------------------------- +151: Ran 60 tests in 18.462s +151: +151: OK +182: [04:04:21] 182: 182: **** 182: Pre-condition Violation @@ -23473,7 +24206,7 @@ 182: Failed Expression: from < static_cast(size()) 182: **** 182: -182: .[07:35:00] +182: .[04:04:21] 182: 182: **** 182: Pre-condition Violation @@ -23482,63 +24215,100 @@ 182: Failed Expression: from < static_cast(size()) 182: **** 182: -128: [07:35:00] Rep: 60 Mol:14 -128: [07:35:00] Rep: 60 Mol:18 -143/223 Test #87: pyChemReactionEnumerations ............. Passed 2.49 sec -test 185 - Start 185: pyTestMultithreadedMolSupplier +163/223 Test #151: pyFMCS ................................. Passed 19.90 sec +test 183 + Start 183: pyTestSGroups -185: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" -185: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -185: Test timeout computed to be: 1500 -128: [07:35:00] Rep: 60 Mol:22 -128: [07:35:00] Rep: 60 Mol:26 -128: [07:35:00] Rep: 60 Mol:30 -147: [07:35:00] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U +183: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testSGroups.py" +183: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +183: Test timeout computed to be: 1500 +158: Randomness seeded to: 2015006241 +158: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/data/chembl_1907596.smi +174: .................. +174: ---------------------------------------------------------------------- +174: Ran 18 tests in 4.908s +174: +174: OK +180: ..............[04:04:21] SMARTS Parse Error: syntax error while parsing: fiib +180: [04:04:21] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +180: ....[04:04:21] ERROR: Problems encountered parsing data fields +180: [04:04:21] ERROR: moving to the beginning of the next molecule +180: [04:04:21] ERROR: Problems encountered parsing data fields +180: [04:04:21] ERROR: moving to the beginning of the next molecule +180: [04:04:21] Spurious data before the first property will be ignored +180: [04:04:21] Property will be truncated after the first blank line +180: [04:04:21] Property will be truncated after the first blank line +180: [04:04:21] Property will be truncated after the first blank line +180: [04:04:21] ERROR: Problems encountered parsing data fields +180: [04:04:21] ERROR: moving to the beginning of the next molecule +180: [04:04:21] ERROR: Problems encountered parsing data fields +180: [04:04:21] ERROR: moving to the beginning of the next molecule +180: [04:04:21] Spurious data before the first property will be ignored +180: [04:04:21] Property will be truncated after the first blank line +180: [04:04:21] Property will be truncated after the first blank line +180: [04:04:21] Property will be truncated after the first blank line +180: [04:04:21] ERROR: Problems encountered parsing data fields +180: [04:04:21] ERROR: moving to the beginning of the next molecule +180: [04:04:21] Property will be truncated after the first blank line +180: [04:04:21] ERROR: Problems encountered parsing data fields +180: [04:04:21] ERROR: moving to the beginning of the next molecule +180: [04:04:21] Property will be truncated after the first blank line +180: .[04:04:21] SMILES Parse Error: syntax error while parsing: fail +180: [04:04:21] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +180: [04:04:21] ERROR: Smiles parse error on line 2 +180: [04:04:21] ERROR: Cannot create molecule from : 'fail' +180: >>> This may result in an infinite loop. It should finish almost instantly +180: <<< OK, it finished. +180: ............[04:04:21] Explicit valence for atom # 1 C, 5, is greater than permitted +164/223 Test #174: pyRGroupDecomposition .................. Passed 6.15 sec +test 184 + Start 184: pyTestThreads + +184: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testThreads.py" +184: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +184: Test timeout computed to be: 1500 +168: [04:04:21] ------------------------------------- +168: [04:04:21] testing TautomerPatternHolder +180: ............[04:04:21] non-ring atom 0 marked aromatic +180: [04:04:21] non-ring atom 0 marked aromatic +180: [04:04:21] +180: +180: **** +180: Range Error +180: idx +180: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp +180: Failed Expression: 12 < 6 +180: **** +180: +180: [04:04:21] non-ring atom 0 marked aromatic +180: [04:04:21] non-ring atom 0 marked aromatic +180: [04:04:21] +180: +180: **** +180: Range Error +180: idx +180: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp +180: Failed Expression: 12 < 6 +180: **** +180: 183: ............. 183: ---------------------------------------------------------------------- -183: Ran 13 tests in 0.054s +183: Ran 13 tests in 0.026s 183: 183: OK 183: Testing SubstanceGroups wrapper -147: file testGithub4238_1.png gave hash 1562907664U not the expected 3410617836U -135: [07:35:00] Molecule does not have explicit Hs. Consider calling AddHs() -147: file testGithub4323_1.png gave hash 3600756148U not the expected 3723958844U -106: =>start test 1 WHIM custom -106: [07:35:00] test on : 365 molecules done -144/223 Test #177: pyMolInterchange ....................... Passed 0.77 sec -test 186 - Start 186: pyTestPropertyLists - -186: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testPropertyLists.py" -186: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -186: Test timeout computed to be: 1500 -145/223 Test #183: pyTestSGroups .......................... Passed 0.57 sec -test 187 - Start 187: pyCDXMLTest +180: ...............[04:04:22] 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. +180: [04:04:22] 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. +165/223 Test #183: pyTestSGroups .......................... Passed 0.62 sec +test 185 + Start 185: pyTestMultithreadedMolSupplier -187: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/test_cdxml.py" -187: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap -187: Test timeout computed to be: 1500 -26: -26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -128: [07:35:00] Rep: 80 Mol:1 -128: [07:35:00] Rep: 80 Mol:5 -128: [07:35:00] Rep: 80 Mol:9 -128: [07:35:00] Rep: 80 Mol:13 -128: [07:35:00] Rep: 80 Mol:17 -128: [07:35:00] Rep: 80 Mol:21 -128: [07:35:00] Rep: 80 Mol:25 -128: [07:35:00] Rep: 80 Mol:29 -181: ...... -181: ---------------------------------------------------------------------- -181: Ran 6 tests in 0.028s -181: -181: OK -180: ..............[07:35:00] SMARTS Parse Error: syntax error while parsing: fiib -180: [07:35:00] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -147: file testGithub4323_3.png gave hash 1951856443U not the expected 2185913679U -182: .[07:35:00] +185: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" +185: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +185: Test timeout computed to be: 1500 +180: ..............[04:04:22] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +180: [04:04:22] Explicit valence for atom # 1 C, 5, is greater than permitted +182: .[04:04:22] 182: 182: **** 182: Range Error @@ -23547,7 +24317,7 @@ 182: Failed Expression: 0 < 0 182: **** 182: -182: .[07:35:00] +182: .[04:04:22] 182: 182: **** 182: Pre-condition Violation @@ -23556,17 +24326,16 @@ 182: Failed Expression: traj.dimension() == 3 182: **** 182: -182: ..[07:35:00] +182: ..[04:04:22] 182: 182: **** -147: [07:35:00] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 182: Pre-condition Violation 182: The trajectory must have dimension == 3 182: Violation occurred on line 154 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: traj.dimension() == 3 182: **** 182: -182: .[07:35:00] +182: .[04:04:22] 182: 182: **** 182: Pre-condition Violation @@ -23575,7 +24344,7 @@ 182: Failed Expression: d_pos 182: **** 182: -182: [07:35:00] +182: [04:04:22] 182: 182: **** 182: Pre-condition Violation @@ -23584,7 +24353,7 @@ 182: Failed Expression: d_trajectory 182: **** 182: -182: .[07:35:00] +182: .[04:04:22] 182: 182: **** 182: Range Error @@ -23593,2104 +24362,555 @@ 182: Failed Expression: 5 < 5 182: **** 182: -128: [07:35:00] Rep: 80 Mol:0 -182: [07:35:00] +182: [04:04:22] 182: 182: **** 182: Range Error 182: pointNum 182: Violation occurred on line 27 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: 10 < 10 -128: [07:35:00] Rep: 80 Mol:4 182: **** 182: -182: .[07:35:00] +182: .[04:04:22] 182: 182: **** 182: Range Error 182: snapshotNum 182: Violation occurred on line 71 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: 5 < 5 -128: [07:35:00] Rep: 80 Mol:8 182: **** 182: -182: [07:35:00] +182: [04:04:22] 182: 182: **** -128: [07:35:00] Rep: 80 Mol:12 182: Pre-condition Violation 182: d_dimension must be == 2 182: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: d_trajectory->dimension() == 2 -128: [07:35:00] Rep: 80 Mol:16 182: **** 182: -182: [07:35:00] +182: [04:04:22] 182: 182: **** 182: Pre-condition Violation 182: d_dimension must be == 2 182: Violation occurred on line 25 in file ./Code/GraphMol/Trajectory/Trajectory.cpp 182: Failed Expression: d_trajectory->dimension() == 2 -128: [07:35:00] Rep: 80 Mol:20 -180: ....[07:35:00] ERROR: Problems encountered parsing data fields -180: [07:35:00] ERROR: moving to the beginning of the next molecule -180: [07:35:00] ERROR: Problems encountered parsing data fields -180: [07:35:00] ERROR: moving to the beginning of the next molecule -180: [07:35:00] Spurious data before the first property will be ignored -180: [07:35:00] Property will be truncated after the first blank line -180: [07:35:00] Property will be truncated after the first blank line -180: [07:35:00] Property will be truncated after the first blank line -146/223 Test #181: pyTestConformerWrap .................... Passed 0.82 sec -test 188 - Start 188: molStandardizeTest - -188: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest -188: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -188: Test timeout computed to be: 1500 -180: [07:35:00] ERROR: Problems encountered parsing data fields -180: [07:35:00] ERROR: moving to the beginning of the next molecule -180: [07:35:00] ERROR: Problems encountered parsing data fields -180: [07:35:00] ERROR: moving to the beginning of the next molecule -180: [07:35:00] Spurious data before the first property will be ignored -180: [07:35:00] Property will be truncated after the first blank line -180: [07:35:00] Property will be truncated after the first blank line -180: [07:35:00] Property will be truncated after the first blank line -180: [07:35:00] ERROR: Problems encountered parsing data fields -180: [07:35:00] ERROR: moving to the beginning of the next molecule -180: [07:35:00] Property will be truncated after the first blank line -180: [07:35:00] ERROR: Problems encountered parsing data fields -180: [07:35:00] ERROR: moving to the beginning of the next molecule -180: [07:35:00] Property will be truncated after the first blank line 182: **** 182: 182: . 182: ---------------------------------------------------------------------- -182: Ran 9 tests in 0.320s +182: Ran 9 tests in 1.052s 182: 182: OK 182: Testing Trajectory wrapper -128: [07:35:00] Rep: 80 Mol:24 -128: [07:35:00] Rep: 80 Mol:28 -180: .[07:35:00] SMILES Parse Error: syntax error while parsing: fail -180: [07:35:00] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -180: [07:35:00] ERROR: Smiles parse error on line 2 -180: [07:35:00] ERROR: Cannot create molecule from : 'fail' -180: >>> This may result in an infinite loop. It should finish almost instantly -180: <<< OK, it finished. -147/223 Test #182: pyTestTrajectory ....................... Passed 0.87 sec +168: [04:04:22] ------------------------------------- +168: [04:04:22] testSegFaultInHolder +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] [04:04:22] SMILES Parse Error: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[04:04:22] [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: [04:04:22] Failed parsing SMILES 'dsafsdf'SMILES Parse Error: syntax error while parsing: dsafsdf +168: for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILESsyntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[04:04:22] for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error[04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: SMILESsyntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: Parse Error: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error[04:04:22] SMILES Parse Error: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: while parsing: dsafsdf +168: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: '[04:04:22] SMILES Parse Error: +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [04:04:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [04:04:22] ------------------------------------- +168: [04:04:22] Results do not depend on numThreads +166/223 Test #182: pyTestTrajectory ....................... Passed 2.34 sec +test 186 + Start 186: pyTestPropertyLists + +186: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testPropertyLists.py" +186: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +186: Test timeout computed to be: 1500 +185: .s. +185: ---------------------------------------------------------------------- +185: Ran 3 tests in 0.519s +185: +185: OK (skipped=1) +185: Testing Smiles and SD MultithreadedMolSupplier +186: [04:04:23] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +186: [04:04:23] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +186: [04:04:23] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +186: .[04:04:23] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +186: [04:04:23] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +186: [04:04:23] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +186: ...[04:04:23] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +186: [04:04:23] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +186: [04:04:23] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +186: . +186: ---------------------------------------------------------------------- +186: Ran 5 tests in 0.038s +186: +186: OK +167/223 Test #185: pyTestMultithreadedMolSupplier ......... Passed 1.83 sec +test 187 + Start 187: pyCDXMLTest + +187: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/test_cdxml.py" +187: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap +187: Test timeout computed to be: 1500 +168/223 Test #186: pyTestPropertyLists .................... Passed 1.22 sec +test 188 + Start 188: molStandardizeTest + +188: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest +188: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +188: Test timeout computed to be: 1500 +171: iterative +187: . +187: ---------------------------------------------------------------------- +187: Ran 1 test in 0.029s +187: +187: OK +169/223 Test #187: pyCDXMLTest ............................ Passed 1.98 sec test 189 Start 189: molNormalizeTest 189: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 189: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 189: Test timeout computed to be: 1500 -180: ............[07:35:00] Explicit valence for atom # 1 C, 5, is greater than permitted -128: [07:35:00] Rep: 80 Mol:2 -128: [07:35:00] Rep: 80 Mol:6 -128: [07:35:00] Rep: 80 Mol:10 -128: [07:35:00] Rep: 80 Mol:14 -128: [07:35:00] Rep: 80 Mol:18 -128: [07:35:00] Rep: 80 Mol:22 -128: [07:35:00] Rep: 80 Mol:26 -128: [07:35:00] Rep: 80 Mol:30 -180: ............[07:35:00] non-ring atom 0 marked aromatic -180: [07:35:00] non-ring atom 0 marked aromatic -180: [07:35:00] -180: -180: **** -180: Range Error -180: idx -180: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp -180: Failed Expression: 12 < 6 -180: **** -180: -180: [07:35:00] non-ring atom 0 marked aromatic -180: [07:35:00] non-ring atom 0 marked aromatic -189: [07:35:00] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -180: [07:35:00] -180: -180: **** -180: Range Error -180: idx -180: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp -180: Failed Expression: 12 < 6 -180: **** -180: -180: ...............[07:35:00] 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. -111: =>start test GETAWAY -111: [07:35:00] test on : 365 molecules done -180: [07:35:00] 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. -148/223 Test #111: testGETAWAY ............................ Passed 2.75 sec +189: [04:04:26] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +189: [04:04:26] Initializing Normalizer +189: [04:04:26] Running Normalizer +189: [04:04:26] Rule applied: BrokenazidetoN=N+=N- +189: [04:04:26] Initializing Normalizer +189: [04:04:26] Running Normalizer +189: [04:04:26] Initializing Normalizer +189: [04:04:26] Running Normalizer +170/223 Test #189: molNormalizeTest ....................... Passed 0.46 sec test 190 Start 190: molValidateTest 190: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest 190: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 190: Test timeout computed to be: 1500 -138: 2030076355 -135: [07:35:00] Molecule does not have explicit Hs. Consider calling AddHs() -180: ..............[07:35:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -180: [07:35:00] Explicit valence for atom # 1 C, 5, is greater than permitted -189: [07:35:00] Initializing Normalizer -189: [07:35:00] Running Normalizer -189: [07:35:00] Rule applied: BrokenazidetoN=N+=N- -189: [07:35:00] Initializing Normalizer -189: [07:35:00] Running Normalizer -189: [07:35:00] Initializing Normalizer -189: [07:35:00] Running Normalizer -149/223 Test #189: molNormalizeTest ....................... Passed 0.18 sec +146: Done +146: ----------------- Test Github #781: Rendering single-atom molecules +171/223 Test #190: molValidateTest ........................ Passed 0.22 sec test 191 Start 191: molChargeTest 191: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest 191: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 191: Test timeout computed to be: 1500 -187: . -187: ---------------------------------------------------------------------- -187: Ran 1 test in 0.026s -187: -187: OK -150/223 Test #190: molValidateTest ........................ Passed 0.09 sec -test 192 - Start 192: molTautomerTest - -192: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest -192: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -192: Test timeout computed to be: 1500 -151/223 Test #38: hanoiTest .............................. Passed 3.27 sec -test 193 - Start 193: molStandardizeSmallTest - -193: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest -193: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -193: Test timeout computed to be: 1500 -150: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -150: Time elapsed 0.000 seconds -150: -150: test32() -150: 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 -150: Time elapsed 0.068 seconds -150: -150: test190() -150: 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 -150: Time elapsed 0.010 seconds -150: -150: test3() -150: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -150: Time elapsed 0.015 seconds -150: -150: testSimpleFast() -150: 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 -150: Time elapsed 0.113 seconds -150: -150: testSimple() -150: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -150: Time elapsed 0.108 seconds -150: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -150: Time elapsed 0.154 seconds -150: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -150: Time elapsed 0.113 seconds -150: -150: testSegFault() -150: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -150: Time elapsed 0.011 seconds -150: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -150: Time elapsed 0.031 seconds -150: 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 -150: Time elapsed 0.026 seconds -150: -150: testThreshold() -150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -150: Time elapsed 0.000 seconds -150: -150: testRing1() -150: 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 -150: Time elapsed 0.569 seconds -150: 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 -150: Time elapsed 0.489 seconds -150: 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 -150: Time elapsed 0.450 seconds -150: -150: testAtomCompareIsotopes() -150: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds -150: Time elapsed 0.000 seconds -150: -150: testAtomCompareAnyAtom() -150: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -150: Time elapsed 0.000 seconds -150: -150: testAtomCompareAnyAtom() -150: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -150: Time elapsed 0.000 seconds -150: -150: testAtomCompareAnyAtom() -150: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds -150: Time elapsed 0.000 seconds -150: -150: testAtomCompareAnyAtom() -150: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds -150: Time elapsed 0.000 seconds -150: -150: testJnk1LigandsDistance() -150: 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 -150: Time elapsed 0.014 seconds -150: 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 -152/223 Test #193: molStandardizeSmallTest ................ Passed 0.07 sec -test 194 - Start 194: molFragmentTest - -194: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest -194: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -194: Test timeout computed to be: 1500 -153/223 Test #187: pyCDXMLTest ............................ Passed 0.51 sec -test 195 - Start 195: molStandardizeCatchTest - -195: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest -195: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -195: Test timeout computed to be: 1500 -154/223 Test #191: molChargeTest .......................... Passed 0.12 sec -test 196 - Start 196: pyMolStandardize - -196: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" -196: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap -196: Test timeout computed to be: 1500 -128: [07:35:00] done -128: [07:35:00] ------------------------------------- -128: [07:35:00] Test MMFF multithreading2 -186: [07:35:00] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -186: [07:35:00] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -186: [07:35:00] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -186: .[07:35:00] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -186: [07:35:00] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -186: [07:35:00] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -186: ...[07:35:00] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -186: [07:35:00] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -186: [07:35:00] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -186: . -186: ---------------------------------------------------------------------- -186: Ran 5 tests in 0.019s -186: -186: OK -130: [07:35:00] done -130: [07:35:00] ------------------------------------- -130: [07:35:00] Test UFF multithreading2 -185: .s. -185: ---------------------------------------------------------------------- -185: Ran 3 tests in 0.222s -185: -185: OK (skipped=1) -185: Testing Smiles and SD MultithreadedMolSupplier -194: [07:35:00] SMARTS Parse Error: syntax error while parsing: [Cl -194: [07:35:00] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -155/223 Test #194: molFragmentTest ........................ Passed 0.14 sec -test 197 - Start 197: testScaffoldNetwork - -197: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork -197: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork -197: Test timeout computed to be: 1500 -156/223 Test #186: pyTestPropertyLists .................... Passed 0.67 sec -test 198 - Start 198: pyScaffoldNetwork - -198: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" -198: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -198: Test timeout computed to be: 1500 -150: Time elapsed 0.001 seconds -150: -150: test18() -150: 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 -150: 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 -150: Time elapsed 0.016 seconds -150: -150: test504() -150: 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 -150: 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 -150: Time elapsed 0.214 seconds -150: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -150: Time elapsed 0.001 seconds -150: 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 -150: Time elapsed 0.093 seconds -150: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds -150: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0047 seconds. bond[0]=6 -150: STATISTICS: -150: Total Growing Steps = 1, MCS found on 1 step, for 0.0047 seconds -150: Initial Seeds = 1, Mismatched 0 -150: Inspected Seeds = 2 -150: Rejected by BestSize = 0 -150: IndividualBondExcluded = 0 -150: MatchCheck Seeds = 2 -150: MatchCalls = 2 -150: MatchFound = 1 -150: fastMatchCalls = 1 -150: fastMatchFound = 0 -150: slowMatchCalls = 2 -150: slowMatchFound = 1 -150: DupCacheFound = 0 0 matched, 0 mismatched -150: HashCache size = 1 keys -150: HashCache size = 1 entries -150: FindHashInCache = 2 -150: HashFoundInCache= 0 -150: ExactMatchCalls = 0 -150: ExactMatchFound = 0 -150: Time elapsed 0.005 seconds -150: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 -150: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 -150: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 -150: res sub = 1 size=3 -150: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -150: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 -150: res sub = 1 size=3 -150: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -150: test target = CC[C@H](F)Cl query = CCC useChirality = 0 -150: res sub = 1 size=3 -150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -150: test target = CC[C@H](F)Cl query = CCC useChirality = 1 -150: res sub = 1 size=3 -150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -150: test target = CCC(F)Cl query = CC useChirality = 0 -150: res sub = 1 size=2 -150: MCS: [#6]-[#6] 2 atoms, 1 bonds -150: test target = CCC(F)Cl query = CC useChirality = 1 -150: res sub = 1 size=2 -150: MCS: [#6]-[#6] 2 atoms, 1 bonds -150: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 -150: res sub = 1 size=4 -150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -150: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 -157/223 Test #185: pyTestMultithreadedMolSupplier ......... Passed 0.97 sec -test 199 - Start 199: pyScaffoldNetworkPickling - -199: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" -199: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -199: Test timeout computed to be: 1500 -150: res sub = 1 size=4 -150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -150: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 -150: res sub = 1 size=4 -150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -150: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 -150: res sub = 1 size=4 -150: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -150: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 -150: res sub = 0 size=0 -150: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -150: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 -150: res sub = 0 size=0 -150: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -150: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 -150: res sub = 1 size=4 -150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -150: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 -150: res sub = 1 size=4 -150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -150: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 -150: res sub = 1 size=4 -150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -150: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 -150: res sub = 1 size=4 -150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -150: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 -150: res sub = 1 size=4 -150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -150: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 -150: res sub = 0 size=0 -150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -150: test target = OC(F)CCl query = OC(F)C useChirality = 0 -150: res sub = 1 size=4 -150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -150: test target = OC(F)CCl query = OC(F)C useChirality = 1 -150: res sub = 1 size=4 -150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -150: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 -150: res sub = 1 size=4 -150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -150: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 -150: res sub = 0 size=0 -150: MCS: [#9] 1 atoms, 0 bonds -150: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 -150: res sub = 1 size=4 -150: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -150: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 -150: res sub = 0 size=0 -150: MCS: [#9] 1 atoms, 0 bonds -150: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 -150: res sub = 1 size=3 -150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -150: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 -150: res sub = 1 size=3 -150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -150: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 -150: res sub = 1 size=3 -150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -150: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 -150: res sub = 1 size=3 -150: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -150: -150: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> -150: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 -150: res sub = 1 size=3 -150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -150: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 -150: res sub = 1 size=3 -150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -150: done -195: Randomness seeded to: 2462257919 -195: * - * - * - * m1 -135: [07:35:01] Molecule does not have explicit Hs. Consider calling AddHs() -195: * - * - * - * m2 -195: * - * - * - * m1 -195: * - * - * - * m2 -159: ........ -159: ---------------------------------------------------------------------- -159: Ran 8 tests in 2.050s -159: -159: OK -195: [07:35:01] Can't kekulize mol. Unkekulized atoms: 3 7 -195: [07:35:01] Can't kekulize mol. Unkekulized atoms: 3 8 -195: [07:35:01] Can't kekulize mol. Unkekulized atoms: 2 3 4 -128: [07:35:01] done -128: [07:35:01] ------------------------------------- -128: [07:35:01] Test MMFF multithreading3 -156: ......... -156: ---------------------------------------------------------------------- -156: Ran 9 tests in 2.294s -156: -156: OK -158/223 Test #159: pyMolDraw2D ............................ Passed 2.57 sec -test 200 - Start 200: testMolEnumerator - -200: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator -200: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator -200: Test timeout computed to be: 1500 -130: [07:35:01] done -130: [07:35:01] ------------------------------------- -130: [07:35:01] Test UFF multithreading3 -147: file testFlexiCanvas.2a.png gave hash 3809318030U not the expected 3217758043U -147: file testFlexiCanvas.2b.png gave hash 1941040420U not the expected 4070063910U -159/223 Test #156: pyMMPA ................................. Passed 2.66 sec -test 201 - Start 201: pyMolEnumerator - -201: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" -201: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap -201: Test timeout computed to be: 1500 -134: [07:35:01] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -147: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U -200: Randomness seeded to: 1216860012 -200: [07:35:01] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -200: =============================================================================== -200: All tests passed (321 assertions in 16 test cases) -200: -160/223 Test #200: testMolEnumerator ...................... Passed 0.24 sec -test 202 - Start 202: testAbbreviations - -202: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations -202: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations -202: Test timeout computed to be: 1500 -147: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U -147: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U -147: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U -198: ....... -198: ---------------------------------------------------------------------- -198: Ran 7 tests in 0.047s -198: -198: OK -147: file testGithub4764.sz1.png gave hash 1936053216U not the expected 98827714U -134: [07:35:01] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -64: [07:35:01] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -64: [07:35:01] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -202: Randomness seeded to: 3211858611 -202: [07:35:01] SMARTS Parse Error: syntax error while parsing: *fail -202: [07:35:01] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -147: file testGithub4764.sz2.png gave hash 518440428U not the expected 89252465U -161/223 Test #198: pyScaffoldNetwork ...................... Passed 0.66 sec -test 203 - Start 203: pyAbbreviations - -203: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" -203: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap -203: Test timeout computed to be: 1500 -202: [07:35:01] no suitable SubstanceGroups found -202: =============================================================================== -202: All tests passed (195 assertions in 12 test cases) -202: -133: building molecules -162/223 Test #202: testAbbreviations ...................... Passed 0.08 sec -test 204 - Start 204: generalizedSubstructCatch - -204: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch -204: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct -204: Test timeout computed to be: 1500 -133: generating reference data -128: [07:35:01] done -128: [07:35:01] ------------------------------------- -128: [07:35:01] Testing github 162: Incorrect SMILES after MMFF parameterization . -128: [07:35:01] done -128: [07:35:01] ------------------------------------- -128: [07:35:01] Testing github 224: crash during MMFF parameterization . -128: [07:35:01] done -128: [07:35:01] ------------------------------------- -128: [07:35:01] Testing github6728: crash due to missing stretch-bend params. -163/223 Test #128: testMMFFForceFieldHelpers .............. Passed 3.54 sec -test 205 - Start 205: pyGeneralizedSubstruct - -205: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" -205: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap -205: Test timeout computed to be: 1500 -199: . -199: ---------------------------------------------------------------------- -199: Ran 1 test in 0.015s -199: -199: OK -138: 959503528 -138: =============================================================================== -138: All tests passed (73 assertions in 3 test cases) -138: -134: [07:35:01] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -130: [07:35:01] done -130: [07:35:01] ------------------------------------- -130: [07:35:01] Testing GitHubIssue62. -164/223 Test #138: molAlignCatchTest ...................... Passed 3.35 sec -test 206 - Start 206: testQuery - -206: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Query/testQuery -206: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Query -206: Test timeout computed to be: 1500 -130: [07:35:01] beta-lactam 39.6387 -130: [07:35:01] cyclopropanone 174.698 -206: Query -206: Query2 -206: Equality -206: Greater -206: GreaterEqual -206: Less -206: LessEqual -206: Open Range -206: Closed Range -206: Float -206: With Tolerance -206: Set -206: And -206: Or -206: XOr -206: pointer and copy foo -206: Set2 -147: file testGithub4764.sz3.png gave hash 1437648833U not the expected 148503574U -165/223 Test #206: testQuery .............................. Passed 0.01 sec -test 207 - Start 207: testMatCalc - -207: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc -207: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc -207: Test timeout computed to be: 1500 -130: [07:35:01] aziridine 337.986 -130: [07:35:01] aziridinone 115.248 -130: [07:35:01] isobutene 2.48217 -130: [07:35:01] acetone 1.91788 -207: 1.68022e+08 -207: 1.73149e+08 -207: 1.05549e+08 -207: 7.20603e+07 -207: 1.41535e+08 -207: 1.08592e+08 -207: 1.11334e+08 -207: 2.05553e+08 -207: 1.54962e+08 -207: 8.08231e+07 -207: 5.61421e+07 -207: 1.28874e+08 -207: 1.59011e+08 -207: 8.69902e+07 -207: 1.31367e+08 -207: 2.27389e+08 -207: 1.60289e+08 -207: 7.79813e+07 -207: 1.61001e+08 -207: 2.07599e+08 -207: 2.24432e+08 -207: 1.39725e+08 -207: 2.42614e+08 -207: 1.77578e+08 -207: 1.05908e+08 -207: 9.06742e+07 -207: 1.8087e+08 -207: 1.98182e+08 -207: 2.03052e+08 -207: 1.7673e+08 -207: 9.32798e+07 -207: 1.37969e+08 -207: 1.83778e+08 -207: 2.1228e+08 -207: 5.06157e+07 -207: 1.566e+08 -207: 2.37142e+08 -207: 1.49345e+08 -207: 7.05819e+07 -207: 1.71633e+08 -207: 1.96817e+08 -207: 2.18246e+08 -207: 9.49496e+07 -207: 2.25618e+08 -207: 1.30219e+08 -166/223 Test #207: testMatCalc ............................ Passed 0.01 sec -test 208 - Start 208: pyMatCalc - -208: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" -208: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap -208: Test timeout computed to be: 1500 -130: [07:35:01] cyclopentanone 10.1648 -130: [07:35:01] cyclopropene 99.4921 -130: [07:35:01] cyclobutene 41.0156 -130: [07:35:01] cyclopropane 267.236 -147: file testGithub_5061.svg gave hash 4026821599U not the expected 83338095U -130: [07:35:01] gamma-lactam 15.7471 -167/223 Test #199: pyScaffoldNetworkPickling .............. Passed 0.60 sec -test 209 - Start 209: testSimDivPickers - -209: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/testSimDivPickers -209: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers -209: Test timeout computed to be: 1500 -209: [07:35:01] ------------------------------------- -209: [07:35:01] Testing github issue 1421: MaxMinPicker picking non-existent element. -209: [07:35:01] Done -209: [07:35:01] ------------------------------------- -209: [07:35:01] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -209: [07:35:01] Done -168/223 Test #209: testSimDivPickers ...................... Passed 0.02 sec -test 210 - Start 210: pickersTestsCatch - -210: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/pickersTestsCatch -210: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers -210: Test timeout computed to be: 1500 -64: ---------------------------------- -64: ---------------------------------- -64: [07:35:01] -64: -64: **** -64: Pre-condition Violation -64: rlabel out of range for MDL files -64: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp -64: Failed Expression: rlabel >= 0 && rlabel < 100 -64: **** -64: -64: [07:35:01] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -130: [07:35:01] trans-2,3-diphenylcyclopropan-1-one 203.398 -147: file github5383_1.svg gave hash 2850811663U not the expected 3666750661U -147: file github5383_2.svg gave hash 1346330069U not the expected 0U -130: [07:35:01] cis-2,3-diphenylcyclopropan-1-one 206.852 -147: file github5383_1.png gave hash 3128184037U not the expected 992803933U -147: file acs1996_1.png gave hash 1346742279U not the expected 2957839025U -130: [07:35:01] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -147: file acs1996_2.png gave hash 806461087U not the expected 2664798808U -130: [07:35:01] cyclopropylidencyclobutane 218.879 -147: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U -201: ... -201: ---------------------------------------------------------------------- -201: Ran 3 tests in 0.015s -201: -201: OK -130: [07:35:01] diphenylmethylidencyclobutane 79.6139 -130: [07:35:01] done -130: [07:35:01] ------------------------------------- -130: [07:35:01] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -130: [07:35:01] done -130: [07:35:01] ------------------------------------- -174: .................. -174: ---------------------------------------------------------------------- -174: Ran 18 tests in 1.955s -174: -174: OK -130: [07:35:01] Test square planar complexes -130: [07:35:01] done -130: [07:35:01] ------------------------------------- -130: [07:35:01] Test octahedral complexes -130: [07:35:01] done -169/223 Test #130: testUFFForceFieldHelpers ............... Passed 3.72 sec -test 211 - Start 211: pySimDivPickers - -211: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/testPickers.py" -211: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap -211: Test timeout computed to be: 1500 -147: [07:35:01] 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. -134: [07:35:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -210: Randomness seeded to: 2522949967 -210: =============================================================================== -210: All tests passed (21267 assertions in 1 test case) -210: -170/223 Test #210: pickersTestsCatch ...................... Passed 0.14 sec -test 212 - Start 212: pyRanker - -212: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/testRanker.py" -212: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap -212: Test timeout computed to be: 1500 -204: Randomness seeded to: 1845426689 -204: =============================================================================== -204: All tests passed (180 assertions in 10 test cases) -204: -171/223 Test #204: generalizedSubstructCatch .............. Passed 0.28 sec -test 213 - Start 213: testChemicalFeatures - -213: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures -213: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures -213: Test timeout computed to be: 1500 -134: [07:35:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -147: file bond_highlights_8.svg gave hash 682598716U not the expected 2956924065U -213: ----------------------------------------- -213: Test1 -213: Done -172/223 Test #201: pyMolEnumerator ........................ Passed 0.58 sec -173/223 Test #213: testChemicalFeatures ................... Passed 0.01 sec -test 214 - Start 214: pyFeatures - -214: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap/testFeatures.py" -214: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap -214: Test timeout computed to be: 1500 -test 215 - Start 215: pythonTestDbCLI - -215: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Projects/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/Projects" -215: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Projects -215: Test timeout computed to be: 1500 -174/223 Test #174: pyRGroupDecomposition .................. Passed 2.52 sec -test 216 - Start 216: pythonTestDirRoot - -216: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit" -216: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit -216: Test timeout computed to be: 1500 -134: [07:35:01] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -175/223 Test #40: resMolSupplierTest ..................... Passed 4.50 sec -test 217 - Start 217: pythonTestDirML - -217: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/ML/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/ML" -217: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit -217: Test timeout computed to be: 1500 -203: ....... -203: ---------------------------------------------------------------------- -203: Ran 7 tests in 0.022s -203: -203: OK -147: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U -176/223 Test #203: pyAbbreviations ........................ Passed 0.43 sec -test 218 - Start 218: pythonTestDirDataStructs - -218: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs" -218: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit -218: Test timeout computed to be: 1500 -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test Issue252: Bad definitions for Crippen atom types. -147: file github6504_1.svg gave hash 3649936662U not the expected 1429448598U -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test calculation of ChiVs. -147: file github6504_2.svg gave hash 106020287U not the expected 2871662880U -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test calculation of ChiNs. -147: file github6569_1.svg gave hash 1698514747U not the expected 116573839U -147: file github6569_2.svg gave hash 2778768241U not the expected 2367779037U -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test calculation of HallKierAlpha. -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test calculation of Kappa1. -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test calculation of Kappa2. -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test calculation of Kappa3. -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test Crippen atom type calculations. -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test ring descriptors -147: file lasso_highlights_1.svg gave hash 2411984833U not the expected 689837467U -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test other count descriptors. -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test MQN -147: file lasso_highlights_2.svg gave hash 1109702647U not the expected 348394942U -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test GitHub Issue 56. -100: [07:35:02] WARNING: not removing hydrogen atom without neighbors -100: [07:35:02] WARNING: not removing hydrogen atom without neighbors -100: [07:35:02] WARNING: not removing hydrogen atom without neighbors -100: [07:35:02] WARNING: not removing hydrogen atom without neighbors -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test Github92: Bad Crippen atom type for pyrrole H. -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test Github362: order dependence in Kier-Hall descriptors. -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test calculation of spiro and bridgehead counts. -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test Github694: ExactMolWt ignoring the mass of the electron -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Testing Properties and KitchenSink -64: [07:35:02] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -64: [07:35:02] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -147: file lasso_highlights_3.svg gave hash 2940545227U not the expected 2174136207U -100: [07:35:02] ---Caught keyerror (bad property name)--- -100: [07:35:02] ---Caught stereo value error--- -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test USR Descriptor -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test Github #1973: support P and S terms for TPSA calculation -100: [07:35:02] done -100: [07:35:02] ------------------------------------- -100: [07:35:02] Test Github #2948: Empty molecule has non-zero LabuteASA -100: [07:35:02] done -147: file lasso_highlights_4.svg gave hash 3276894790U not the expected 1265047504U -177/223 Test #100: testDescriptors ........................ Passed 4.44 sec -test 219 - Start 219: pythonTestDirDbase - -219: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase" -219: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit -219: Test timeout computed to be: 1500 -147: file lasso_highlights_5.svg gave hash 2028645321U not the expected 35778943U -147: file lasso_highlights_6.svg gave hash 1732575234U not the expected 1359376880U -147: file lasso_highlights_7.svg gave hash 1593492996U not the expected 773081917U -196: .....[07:35:02] Tautomer enumeration stopped at 292 tautomers: max transforms reached -64: [07:35:02] Empty atom list: 'M ALS 1 0 F' on line 8. -64: de_DE.UTF-8 -64: [07:35:02] ------------------------------------- -64: [07:35:02] Test multithreading Locale Switching -192: [07:35:02] Tautomer enumeration stopped at 292 tautomers: max transforms reached -214: .. -214: ---------------------------------------------------------------------- -214: Ran 2 tests in 0.001s -214: -214: OK -214: Testing ChemicalFeatures Wrapper code: -135: [07:35:02] Molecule does not have explicit Hs. Consider calling AddHs() -147: file bad_lasso_1.svg gave hash 1431427975U not the expected 1183031575U -147: =============================================================================== -147: All tests passed (6525 assertions in 94 test cases) -147: -178/223 Test #147: moldraw2DTestCatch ..................... Passed 3.79 sec -test 220 - Start 220: pythonTestDirSimDivFilters - -220: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters" -220: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit -220: Test timeout computed to be: 1500 -211: [07:35:02] the useCache argument is deprecated and ignored -64: [07:35:02] Test multithreading (Done) -64: [07:35:02] ------------------------------------- -212: ..[07:35:02] -212: -212: **** -212: Invariant Violation -212: Can't rank more bits than the ensemble size -212: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp -212: Failed Expression: num <= dp_maskBits->getNumOnBits() -212: **** -212: -212: ... -212: ---------------------------------------------------------------------- -212: Ran 5 tests in 0.022s -212: -212: OK -179/223 Test #214: pyFeatures ............................. Passed 0.37 sec -test 221 - Start 221: pythonTestDirVLib - -221: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/VLib/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/VLib" -221: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit -221: Test timeout computed to be: 1500 -64: *************************************** -64: *************************************** -64: [07:35:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -64: [07:35:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -196: [07:35:02] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -180/223 Test #212: pyRanker ............................... Passed 0.43 sec -test 222 - Start 222: pythonTestSping - -222: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/sping" -222: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit -222: Test timeout computed to be: 1500 -64: [07:35:02] bond with order 0 found on line 7. This is not part of the MDL specification. -64: [07:35:02] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -64: [07:35:02] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -64: [07:35:02] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:21: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML import BuildComposite -64: generating smiles -64: 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 -64: converting back -64: check isomorphism -205: ....... -205: ---------------------------------------------------------------------- -205: Ran 7 tests in 0.189s -205: -205: OK -135: [07:35:02] Molecule does not have explicit Hs. Consider calling AddHs() -181/223 Test #188: molStandardizeTest ..................... Passed 1.95 sec -test 223 - Start 223: pythonTestDirChem - -223: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Chem" "--buildType" "None" -223: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit/Chem -223: Test timeout computed to be: 1500 -182/223 Test #205: pyGeneralizedSubstruct ................. Passed 0.77 sec -219: .. -219: ---------------------------------------------------------------------- -219: Ran 2 tests in 0.050s -219: -219: OK -211: ...[07:35:02] the useCache argument is deprecated and ignored -211: [07:35:02] the useCache argument is deprecated and ignored -211: .[07:35:02] the useCache argument is deprecated and ignored -218: ....... -218: ---------------------------------------------------------------------- -218: Ran 7 tests in 0.023s -218: -218: OK -208: ..... -208: ---------------------------------------------------------------------- -208: Ran 5 tests in 0.334s -208: -208: OK -216: ......................... -216: ---------------------------------------------------------------------- -216: Ran 25 tests in 0.396s -216: -216: OK -183/223 Test #208: pyMatCalc .............................. Passed 0.84 sec -196: .[07:35:02] Tautomer enumeration stopped at 63 tautomers: canceled -196: Enumeration was canceled due to timeout (50 ms) -221: ............. -221: ---------------------------------------------------------------------- -221: Ran 13 tests in 0.035s -221: -221: OK -184/223 Test #216: pythonTestDirRoot ...................... Passed 0.67 sec -135: [07:35:02] Molecule does not have explicit Hs. Consider calling AddHs() -150: [07:35:02] The provided InitialSeed is not an MCS and will be ignored -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:83: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: refCompos = pickle.load(pklF) -158: Randomness seeded to: 3297325481 -158: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -219: ........... -219: ---------------------------------------------------------------------- -219: Ran 11 tests in 0.123s -219: -219: OK -192: [07:35:02] Tautomer enumeration stopped at 292 tautomers: max transforms reached -135: [07:35:02] Molecule does not have explicit Hs. Consider calling AddHs() -218: .................................. -218: ---------------------------------------------------------------------- -218: Ran 34 tests in 0.010s -218: -218: OK -197: Randomness seeded to: 1810421622 -197: =============================================================================== -197: All tests passed (269 assertions in 19 test cases) -197: -185/223 Test #197: testScaffoldNetwork .................... Passed 1.95 sec -186/223 Test #220: pythonTestDirSimDivFilters ............. Passed 0.62 sec -137: *********************************************************** -137: Testing O3AAlign -137: --------------------------------- -137: testMMFFO3A -137: -137: --------------------------------- -137: testMMFFO3A with pre-computed dmat and MolHistogram -137: -137: --------------------------------- -137: testMMFFO3A with constraints -137: -137: --------------------------------- -137: testMMFFO3A with variable weight constraints followed by local-only optimization -137: -137: --------------------------------- -137: testCrippenO3A -137: -137: --------------------------------- -137: testCrippenO3A with pre-computed dmat and MolHistogram -137: -137: --------------------------------- -137: testCrippenO3A with constraints -137: -137: --------------------------------- -137: testCrippenO3A with variable weight constraints followed by local-only optimization -137: -137: --------------------------------- -137: testMMFFO3A multithreading -137: -137: generating reference data -192: [07:35:02] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -219: . -219: ---------------------------------------------------------------------- -219: Ran 1 test in 0.001s -219: -219: OK -106: =>start test GETAWAY custom -106: [07:35:03] test on : 365 molecules done -187/223 Test #106: testRDFcustom .......................... Passed 5.31 sec -135: [07:35:03] Molecule does not have explicit Hs. Consider calling AddHs() -219: FF......F...... -219: ====================================================================== -219: FAIL: test1Txt (__main__.TestCase.test1Txt) -219: test reading from a text file -219: ---------------------------------------------------------------------- -219: Traceback (most recent call last): -219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 77, in test1Txt -219: self._confirm(tblName, dbName=self.tempDbName) -219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm -219: assert len(res) == len(colHeads), 'bad number of columns' -219: ^^^^^^^^^^^^^^^^^^^^^^^^^ -219: AssertionError: bad number of columns -219: -219: ====================================================================== -219: FAIL: test3Txt (__main__.TestCase.test3Txt) -219: test reading from a text file including null markers -219: ---------------------------------------------------------------------- -219: Traceback (most recent call last): -219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 87, in test3Txt -219: self._confirm(tblName, dbName=self.tempDbName) -219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm -219: assert len(res) == len(colHeads), 'bad number of columns' -219: ^^^^^^^^^^^^^^^^^^^^^^^^^ -219: AssertionError: bad number of columns -219: -219: ====================================================================== -219: FAIL: test_DatabaseToDatabase (__main__.TestCase.test_DatabaseToDatabase) -219: ---------------------------------------------------------------------- -219: Traceback (most recent call last): -219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 219, in test_DatabaseToDatabase -219: self._confirm(tblName, dbName=self.tempDbName, colHeads=['id', 'val']) -219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm -219: assert len(res) == len(colHeads), 'bad number of columns' -219: ^^^^^^^^^^^^^^^^^^^^^^^^^ -219: AssertionError: bad number of columns -219: -219: ---------------------------------------------------------------------- -219: Ran 15 tests in 0.074s -219: -219: FAILED (failures=3) -223: ....... -223: ---------------------------------------------------------------------- -223: Ran 7 tests in 0.167s -223: -223: OK -192: [07:35:03] Tautomer enumeration stopped at 25 tautomers: canceled -192: Enumeration was canceled due to timeout (50 ms) -135: [07:35:03] Molecule does not have explicit Hs. Consider calling AddHs() -217: ...../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:198: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: refCompos = pickle.load(pklFile) -219: ...... -219: ---------------------------------------------------------------------- -219: Ran 6 tests in 0.006s -219: -219: OK -221: ........... -221: ---------------------------------------------------------------------- -221: Ran 11 tests in 0.111s -221: -221: OK -219: !!! TEST FAILURE: python UnitTestDbUtils.py {} -188/223 Test #219: pythonTestDirDbase .....................***Failed 1.25 sec -.. ----------------------------------------------------------------------- -Ran 2 tests in 0.050s - -OK -........... ----------------------------------------------------------------------- -Ran 11 tests in 0.123s - -OK -. ----------------------------------------------------------------------- -Ran 1 test in 0.001s - -OK -FF......F...... -====================================================================== -FAIL: test1Txt (__main__.TestCase.test1Txt) -test reading from a text file ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 77, in test1Txt - self._confirm(tblName, dbName=self.tempDbName) - File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm - assert len(res) == len(colHeads), 'bad number of columns' - ^^^^^^^^^^^^^^^^^^^^^^^^^ -AssertionError: bad number of columns - -====================================================================== -FAIL: test3Txt (__main__.TestCase.test3Txt) -test reading from a text file including null markers ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 87, in test3Txt - self._confirm(tblName, dbName=self.tempDbName) - File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm - assert len(res) == len(colHeads), 'bad number of columns' - ^^^^^^^^^^^^^^^^^^^^^^^^^ -AssertionError: bad number of columns - -====================================================================== -FAIL: test_DatabaseToDatabase (__main__.TestCase.test_DatabaseToDatabase) ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 219, in test_DatabaseToDatabase - self._confirm(tblName, dbName=self.tempDbName, colHeads=['id', 'val']) - File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm - assert len(res) == len(colHeads), 'bad number of columns' - ^^^^^^^^^^^^^^^^^^^^^^^^^ -AssertionError: bad number of columns - ----------------------------------------------------------------------- -Ran 15 tests in 0.074s - -FAILED (failures=3) -...... ----------------------------------------------------------------------- -Ran 6 tests in 0.006s - -OK -!!! TEST FAILURE: python UnitTestDbUtils.py {} - -215: [07:35:03] INFO: Reading molecules and constructing molecular database. -215: -215: [07:35:03] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -215: -215: [07:35:03] INFO: Processing 10 molecules -215: -217: . -217: ---------------------------------------------------------------------- -217: Ran 6 tests in 0.715s -217: -217: OK -222: .. -222: ---------------------------------------------------------------------- -222: Ran 2 tests in 0.567s -222: -222: OK -211: ....... -211: ---------------------------------------------------------------------- -211: Ran 11 tests in 1.261s -211: -211: OK -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 5.912s -12: -12: OK -215: [07:35:03] INFO: Generating fingerprints and descriptors: -215: -189/223 Test #12: pyBV ................................... Passed 6.16 sec -190/223 Test #221: pythonTestDirVLib ...................... Passed 1.30 sec -218: ..... -218: ---------------------------------------------------------------------- -218: Ran 5 tests in 0.044s -218: -218: OK -26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -191/223 Test #211: pySimDivPickers ........................ Passed 1.72 sec -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:20: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML import ScreenComposite -26: All 191 tests passed -215: [07:35:03] INFO: Finished. -215: -171: iterative -223: ...... -223: ---------------------------------------------------------------------- -223: Ran 6 tests in 0.047s -223: -223: OK -192/223 Test #222: pythonTestSping ........................ Passed 1.50 sec -26: -26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:276: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: compos = pickle.load(pklF) -217: ../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:330: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: compos = pickle.load(pklF) -64: [07:35:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [07:35:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [07:35:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [07:35:03] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [07:35:03] deprecated group abbreviation ignored on line 24 -64: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -64: [07:35:03] -64: -64: **** -64: Post-condition Violation -64: Element 'Mv' not found -64: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -64: Failed Expression: anum > -1 -64: **** -64: -168: [07:35:03] ------------------------------------- -168: [07:35:03] testing PatternHolder -217: .......... -217: ---------------------------------------------------------------------- -217: Ran 12 tests in 0.164s -217: -217: OK -218: ....... -218: ---------------------------------------------------------------------- -218: Ran 7 tests in 0.006s -218: -218: OK -196: Enumeration has completed -196: [07:35:04] Tautomer enumeration stopped at 48 tautomers: canceled -193/223 Test #218: pythonTestDirDataStructs ............... Passed 2.22 sec -168: [07:35:04] ------------------------------------- -168: [07:35:04] testing TautomerPatternHolder -133: validating reference data -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML import AnalyzeComposite -223: ....[07:35:04] -223: -223: **** -223: Pre-condition Violation -223: valence not defined for atoms not associated with molecules -223: Violation occurred on line 411 in file ./Code/GraphMol/Atom.cpp -223: Failed Expression: dp_mol -223: **** -223: -223: . -223: ---------------------------------------------------------------------- -223: Ran 5 tests in 0.031s -223: -223: OK -192: 375 -192: Enumeration has completed -192: [07:35:04] Tautomer enumeration stopped at 48 tautomers: canceled -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:31: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: c1 = pickle.load(pklF) -168: [07:35:04] ------------------------------------- -168: [07:35:04] testSegFaultInHolder -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: dsafsdf -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[07:35:04] [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] [07:35:04] SMILES Parse Error: syntax error[07:35:04] [07:35:04] [07:35:04] -168: dsafsdf[07:35:04] SMILESSMILES Parse Error: SMILES Parse Error: syntax errorsyntax error' while parsing: SMILES Parse Error: while parsing: -168: dsafsdf -168: while parsing: dsafsdf -168: syntax error[07:35:04] dsafsdfSMILES -168: while parsing: SMILES Parse Error: dsafsdf -168: [07:35:04] [07:35:04] [07:35:04] SMILES Parse Error: syntax error while parsing: syntax error[07:35:04] Parse Error: SMILES Parse Error: [07:35:04] [07:35:04] SMILES Parse Error: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'SMILES for input: ' Parse Error: Failed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf'dsafsdf[07:35:04] syntax error while parsing: dsafsdf -168: 'SMILES Parse Error: -168: SMILESsyntax error while parsing: for input: 'dsafsdfdsafsdf' -168: while parsing: for input: ' Parse Error: syntax error while parsing: dsafsdf -168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[07:35:04] SMILES Parse Error: dsafsdf'dsafsdf -168: -168: dsafsdfFailed parsing SMILES 'dsafsdf'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: ' -168: for input: 'dsafsdf -168: [07:35:04] SMILES[07:35:04] [07:35:04] -168: SMILESSMILES Parse Error: dsafsdfsyntax error' while parsing: dsafsdf -168: [07:35:04] -168: SMILES Parse Error: Parse Error: Failed parsing SMILES 'dsafsdf' Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[07:35:04] [07:35:04] syntax errorSMILES Parse Error: [07:35:04] syntax errorSMILESSMILESSMILESdsafsdf for input: 'dsafsdf' -168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: '' while parsing: Parse Error: dsafsdf -168: Failed parsing SMILES 'dsafsdf'dsafsdf' -168: -168: for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[07:35:04] [07:35:04] SMILESSMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] [07:35:04] SMILES Parse Error: dsafsdf Parse Error: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: for input: 'Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: dsafsdfFailed parsing SMILES 'dsafsdf'' for input: ' -168: ' -168: dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] [07:35:04] SMILES Parse Error: syntax error[07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: [07:35:04] SMILES Parse Error: syntax error while parsing: syntax error while parsing: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: dsafsdf -168: [07:35:04] SMILES[07:35:04] Parse Error: Failed parsing SMILES 'dsafsdf'SMILES for input: 'dsafsdf' -168: dsafsdf Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf -168: ' -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -217: . -217: ---------------------------------------------------------------------- -217: Ran 1 test in 0.044s -217: -217: OK -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf[07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILESSMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: [07:35:04] [07:35:04] [07:35:04] [07:35:04] [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: [07:35:04] [07:35:04] [07:35:04] SMILES Parse Error: [07:35:04] [07:35:04] [07:35:04] [07:35:04] SMILES Parse Error: syntax error[07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[07:35:04] Failed parsing SMILES 'dsafsdf' for input: '[07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdfSMILES Parse Error: [07:35:04] syntax error[07:35:04] while parsing: dsafsdf -168: SMILES Parse Error: SMILES Parse Error: [07:35:04] syntax error while parsing: while parsing: dsafsdfdsafsdfSMILES Parse Error: ' for input: 'SMILES Parse Error: syntax errorsyntax errorsyntax error -168: while parsing: SMILES Parse Error: SMILES Parse Error: [07:35:04] SMILESsyntax error Parse Error: SMILES Parse Error: -168: syntax error while parsing: [07:35:04] dsafsdfSMILES Parse Error: syntax error while parsing: -168: dsafsdf -168: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: for input: 'dsafsdf'[07:35:04] while parsing: SMILES while parsing: dsafsdf -168: while parsing: dsafsdfSMILES Parse Error: -168: syntax errordsafsdf[07:35:04] dsafsdf Parse Error: SMILES Parse Error: -168: -168: dsafsdf[07:35:04] ' -168: SMILES Parse Error: -168: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfSMILES Parse Error: syntax errorSMILESFailed parsing SMILES 'dsafsdf'[07:35:04] syntax errorSMILES Parse Error: while parsing: dsafsdfsyntax errordsafsdf while parsing: dsafsdfsyntax error -168: [07:35:04] for input: '[07:35:04] [07:35:04] -168: SMILESSMILES Parse Error: syntax errordsafsdf' Parse Error: ' while parsing: SMILES[07:35:04] while parsing: while parsing: [07:35:04] dsafsdf -168: SMILES Parse Error: syntax error while parsing: dsafsdf[07:35:04] -168: syntax errorsyntax errorSMILES while parsing: dsafsdf -168: dsafsdf Parse Error: Parse Error: Failed parsing SMILES 'dsafsdf' -168: for input: 'dsafsdfSMILESdsafsdfFailed parsing SMILES 'dsafsdf' for input: 'dsafsdf' Parse Error: -168: -168: -168: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'syntax error while parsing: ' -168: dsafsdf -168: -168: for input: ' while parsing: dsafsdfFailed parsing SMILES 'dsafsdf'' -168: for input: 'dsafsdfdsafsdf -168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: -168: ' -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] syntax errorSMILES[07:35:04] [07:35:04] [07:35:04] SMILES[07:35:04] SMILES Parse Error: [07:35:04] while parsing: SMILESdsafsdf Parse Error: Parse Error: SMILESFailed parsing SMILES 'dsafsdf'[07:35:04] -168: SMILES for input: '[07:35:04] Failed parsing SMILES 'dsafsdf' Parse Error: for input: 'Failed parsing SMILES 'dsafsdf'dsafsdf' for input: 'dsafsdf Parse Error: Failed parsing SMILES 'dsafsdf' -168: dsafsdfSMILES' -168: for input: 'dsafsdf' -168: ' -168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES[07:35:04] SMILES Parse Error: syntax error Parse Error: Failed parsing SMILES 'dsafsdf' for input: ' while parsing: dsafsdf -168: dsafsdf' -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: SMILES Parse Error: syntax error while parsing: -168: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -135: .[07:35:04] Molecule does not have explicit Hs. Consider calling AddHs() -137: processing -137: launch :0 -137: launch :1 -137: launch :2 -137: launch :3 -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [07:35:04] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [07:35:04] ------------------------------------- -168: [07:35:04] Results do not depend on numThreads -67: [07:35:04] Finished: testSmiCorrectness() -67: [07:35:04] ----------------------------------------- -67: -67: [07:35:04] -67: ----------------------------------------- -67: [07:35:04] Spurious data before the first property will be ignored -67: [07:35:04] [07:35:04] Property will be truncated after the first blank line -67: Property will be truncated after the first blank line -67: [07:35:04] Property will be truncated after the first blank line -171: bulk -117: [07:35:04] done -117: [07:35:04] ------------------------------------- -117: [07:35:04] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -117: [07:35:04] done -117: [07:35:04] ------------------------------------- -117: [07:35:04] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -117: [07:35:04] done -117: [07:35:04] ------------------------------------- -117: [07:35:04] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -117: [07:35:04] done -117: [07:35:04] ------------------------------------- -117: [07:35:04] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -117: [07:35:04] done -117: [07:35:04] ------------------------------------- -117: [07:35:04] Test unfolded version of RDKFP -117: [07:35:04] ------------------------------------- -117: [07:35:04] Test bitinfo of RDKFP -117: 562: [ 2 ], -117: 709: [ 0 1 ], -117: 1118: [ 0 1 2 ], -117: 1183: [ 1 2 ], -117: 1233: [ 0 1 2 ], -117: 1308: [ 0 ], [ 1 ], -117: 1339: [ 2 ], -117: 1728: [ 1 2 ], -117: 1772: [ 0 ], [ 1 ], -117: 1813: [ 0 1 ], -117: ------------ -117: [07:35:04] ------------------------------------- -117: [07:35:04] Single atoms setting radius 1 bits in Morgan fingerprints -117: [07:35:04] done -117: [07:35:04] ------------------------------------- -117: [07:35:04] Github #879: Pattern fingerprint should set bits for single-atom fragments. -117: [07:35:04] done -117: [07:35:04] ------------------------------------- -117: [07:35:04] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -117: [07:35:04] done -117: [07:35:04] ------------------------------------- -117: [07:35:04] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -117: [07:35:04] done -117: [07:35:04] ------------------------------------- -117: [07:35:04] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -117: [07:35:04] done -117: [07:35:04] ------------------------------------- -117: [07:35:04] Github #2115: BitInfo not complete for RDKFingerprint -117: [07:35:04] done -117: [07:35:04] ------------------------------------- -117: [07:35:04] Github #3723: Fingerprint crash for mols with Zero order bonds -117: [07:35:04] done -194/223 Test #117: testFingerprints ....................... Passed 6.81 sec -196: ....................[07:35:04] Explicit valence for atom # 1 O, 3, is greater than permitted -196: . -196: ---------------------------------------------------------------------- -196: Ran 27 tests in 3.310s -196: -196: OK -196: done -223: .... -223: ---------------------------------------------------------------------- -223: Ran 4 tests in 0.024s -223: -223: OK -151: ........................................[07:35:05] The provided InitialSeed is not an MCS and will be ignored -151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored -151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored -195/223 Test #196: pyMolStandardize ....................... Passed 4.26 sec -151: .[07:35:05] The provided InitialSeed is not an MCS and will be ignored -151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored -151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored -151: .[07:35:05] The provided InitialSeed is not an MCS and will be ignored -151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored -151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored -192: CN=c1cc[nH]cn1 -192: CN=c1ccnc[nH]1 -192: CNc1ccncn1 -192: res: CNc1ccncn1 -192: CN=c1cccc[nH]1 -192: CNc1ccccn1 -192: res: CNc1ccccn1 -151: .[07:35:05] The provided InitialSeed is not an MCS and will be ignored -151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored -215: [07:35:05] INFO: Reading molecules and constructing molecular database. -215: -217: ... -151: [07:35:05] The provided InitialSeed is not an MCS and will be ignored -217: ---------------------------------------------------------------------- -217: Ran 3 tests in 0.002s -217: -217: OK -215: [07:35:05] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -215: -215: [07:35:05] INFO: Processing 163 molecules -215: -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -67: [07:35:05] Finished: testSDCorrectness() -67: [07:35:05] ----------------------------------------- -67: -196/223 Test #67: testMultithreadedMolSupplier ........... Passed 7.64 sec -151: ................. -151: ---------------------------------------------------------------------- -151: Ran 60 tests in 6.286s -151: -151: OK -197/223 Test #151: pyFMCS ................................. Passed 6.72 sec -198/223 Test #192: molTautomerTest ........................ Passed 4.67 sec -223: .. -223: ---------------------------------------------------------------------- -223: Ran 2 tests in 0.012s -223: -223: OK -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -180: ...........................[07:35:05] unable to set wavy bonds for double bonds: 3 -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -180: .........[07:35:05] -180: -180: **** -180: Range Error -180: idx -180: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp -180: Failed Expression: 6 < 5 -180: **** -180: -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:05] INFO: done 100 -215: -195: =============================================================================== -195: All tests passed (18691 assertions in 41 test cases) -195: -199/223 Test #195: molStandardizeCatchTest ................ Passed 4.92 sec -217: ........ -217: ---------------------------------------------------------------------- -217: Ran 8 tests in 0.001s -217: -217: OK -223: ...................... -223: ---------------------------------------------------------------------- -223: Ran 22 tests in 0.039s -223: -223: OK -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML.Composite import Composite -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML.DecTree.DecTree import DecTreeNode as Node -64: [07:35:06] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -64: [07:35:06] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -64: ---------------------------------- -64: ---------------------------------- -64: [07:35:06] -64: -64: **** -64: Pre-condition Violation -64: rlabel out of range for MDL files -64: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp -64: Failed Expression: rlabel >= 0 && rlabel < 100 -64: **** -64: -64: [07:35:06] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -223: .....s.................ss -223: ---------------------------------------------------------------------- -223: Ran 25 tests in 0.115s -223: -223: OK (skipped=3) -146: Done -146: ----------------- Test Github #781: Rendering single-atom molecules 146: Done 146: ----------------- Test 3 146: file test3_1.png gave hash 312151313U not the expected 3984824963U 146: file test3_2.png gave hash 2567824136U not the expected 238321316U -217: .... -217: ---------------------------------------------------------------------- -217: Ran 4 tests in 0.328s -217: -217: OK 146: file test3_3.png gave hash 527793981U not the expected 414888185U -200/223 Test #184: pyTestThreads .......................... Passed 6.44 sec 146: file test3_4.png gave hash 1225446657U not the expected 2265825690U -133: processing -133: launch :0 -133: launch :1 -133: launch :2 -133: launch :3 -64: [07:35:06] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -64: [07:35:06] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' 146: file test3_5.png gave hash 4191147962U not the expected 1911551403U +172/223 Test #191: molChargeTest .......................... Passed 0.42 sec +test 192 + Start 192: molTautomerTest + +192: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest +192: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +192: Test timeout computed to be: 1500 146: file test3_6.png gave hash 628781660U not the expected 577293879U 146: file test3_7.png gave hash 765801686U not the expected 248355372U 146: Done 146: ----------------- Test Github774: upside-down drawings 146: file test774_1.png gave hash 1357227033U not the expected 927423591U -64: [07:35:06] Empty atom list: 'M ALS 1 0 F' on line 8. -201/223 Test #64: fileParsersTest1 ....................... Passed 9.13 sec 146: file test774_2.png gave hash 2459987343U not the expected 1171827286U 146: Done 146: ----------------- Test 9 (molecule legends) 146: file test9_1.svg gave hash 923579170U not the expected 1484349178U 146: Done 146: ----------------- Test Github852: Lines used to wedge bonds are too thick -215: [07:35:06] INFO: Generating fingerprints and descriptors: -215: 146: file test852_1.png gave hash 945814889U not the expected 736085072U 146: file test852_2.png gave hash 1614071321U not the expected 1438089260U 146: ---------------- @@ -25710,6 +24930,14 @@ 146: ----------------- Test Github #953: default color should not be cyan 146: Done 146: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly +171: bulk +173/223 Test #188: molStandardizeTest ..................... Passed 4.03 sec +test 193 + Start 193: molStandardizeSmallTest + +193: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest +193: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +193: Test timeout computed to be: 1500 146: Done 146: ----------------- Test Deuterium, Tritium 146: Done @@ -25722,10 +24950,23 @@ 146: ----------------- Testing drawing a grid of molecules 146: Done 146: ----------------- Testing drawMolecules +174/223 Test #193: molStandardizeSmallTest ................ Passed 0.19 sec +test 194 + Start 194: molFragmentTest + +194: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest +194: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +194: Test timeout computed to be: 1500 146: file test12_1.svg gave hash 2982175789U not the expected 881731720U -180: ...................[07:35:06] Explicit valence for atom # 1 F, 2, is greater than permitted -180: [07:35:06] Explicit valence for atom # 6 F, 2, is greater than permitted -180: [07:35:06] Can't kekulize mol. Unkekulized atoms: 3 4 5 +194: [04:04:28] SMARTS Parse Error: syntax error while parsing: [Cl +194: [04:04:28] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +175/223 Test #194: molFragmentTest ........................ Passed 0.27 sec +test 195 + Start 195: molStandardizeCatchTest + +195: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest +195: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +195: Test timeout computed to be: 1500 146: Done 146: ----------------- Test JSON Configuration 146: Done @@ -25746,7 +24987,6 @@ 146: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list 146: Done 146: ----------------- Testing use of fixed scales for drawing. -180: ...............[07:35:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 146: Done 146: ----------------- Testing rotation of 2D drawing. 146: Done @@ -25765,19 +25005,18 @@ 146: file testGithub2931_3.svg gave hash 1986517899U not the expected 2885834646U 146: Done 146: ----------------- Testing annotation of 2D Drawing. +26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +195: Randomness seeded to: 494387182 +195: * - * - * - * m1 +195: * - * - * - * m2 +195: * - * - * - * m1 +195: * - * - * - * m2 146: file test20_1.png gave hash 3128373795U not the expected 1672353490U +195: [04:04:29] Can't kekulize mol. Unkekulized atoms: 3 7 146: file test20_2.png gave hash 4290694897U not the expected 1073213605U -223: ..s -223: ---------------------------------------------------------------------- -223: Ran 3 tests in 0.143s -223: -223: OK (skipped=1) +195: [04:04:29] Can't kekulize mol. Unkekulized atoms: 3 8 +195: [04:04:29] Can't kekulize mol. Unkekulized atoms: 2 3 4 146: file test20_3.png gave hash 2552889633U not the expected 471234756U -217: ..... -217: ---------------------------------------------------------------------- -217: Ran 5 tests in 0.002s -217: -217: OK 146: file test20_4.png gave hash 1903980179U not the expected 2803490234U 146: Done 146: ----------------- Test 21 - different font @@ -25788,8 +25027,11 @@ 146: Done 146: ----------------- Test Github 3305 - change and scale line widths. 146: file testGithub3305_1.png gave hash 3050910344U not the expected 1801411420U +26: All 191 tests passed 146: file testGithub3305_2.png gave hash 3318976613U not the expected 2904846519U 146: file testGithub3305_3.png gave hash 2285309697U not the expected 2915229647U +26: +26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... 146: file testGithub3305_4.png gave hash 4191147962U not the expected 1911551403U 146: file testGithub3305_5.png gave hash 2872233459U not the expected 614319597U 146: file testGithub3305_5.svg gave hash 911738919U not the expected 3435115096U @@ -25806,24 +25048,25 @@ 146: Done 146: ----------------- Test AND queries 146: Done -202/223 Test #146: moldraw2DTest1 ......................... Passed 8.68 sec -217: ......... -217: ---------------------------------------------------------------------- -217: Ran 9 tests in 0.004s -217: -217: OK +176/223 Test #146: moldraw2DTest1 ......................... Passed 32.60 sec +test 196 + Start 196: pyMolStandardize + +196: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" +196: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap +196: Test timeout computed to be: 1500 +192: [04:04:30] Tautomer enumeration stopped at 292 tautomers: max transforms reached 171: bulk, no symmetry -217: ............ -217: ---------------------------------------------------------------------- -217: Ran 12 tests in 0.002s -217: -217: OK -171: [07:35:07] Relabelling existing label -217: ..... -217: ---------------------------------------------------------------------- -217: Ran 5 tests in 0.017s -217: -217: OK +192: [04:04:32] Tautomer enumeration stopped at 292 tautomers: max transforms reached +192: [04:04:32] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +196: .....[04:04:32] Tautomer enumeration stopped at 292 tautomers: max transforms reached +196: [04:04:33] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +192: [04:04:33] Tautomer enumeration stopped at 21 tautomers: canceled +192: Enumeration was canceled due to timeout (50 ms) +196: .[04:04:33] Tautomer enumeration stopped at 14 tautomers: canceled +196: Enumeration was canceled due to timeout (50 ms) +171: [04:04:34] Relabelling existing label +135: ..[04:04:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 162: VS001: PASSED 162: VS002: PASSED 162: VS003: PASSED @@ -26126,18 +25369,259 @@ 162: VS300: PASSED 162: Check finished: 0 molecules failed. 162: Failed: +168: [04:04:35] ------------------------------------- +168: [04:04:35] Results do not depend on numThreads (all same) +177/223 Test #162: pyCIPLabelsValidation .................. Passed 27.07 sec +test 197 + Start 197: testScaffoldNetwork + +197: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork +197: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork +197: Test timeout computed to be: 1500 +168: [04:04:35] ------------------------------------- +168: [04:04:35] testTautomerQueries +168: [04:04:35] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +168: [04:04:35] ------------------------------------- +168: [04:04:35] github3881 recursive smarts with rings 171: Best mapping -203/223 Test #162: pyCIPLabelsValidation .................. Passed 9.24 sec -168: [07:35:08] ------------------------------------- -168: [07:35:08] Results do not depend on numThreads (all same) -204/223 Test #171: testRGroupDecomp ....................... Passed 9.00 sec -168: [07:35:08] ------------------------------------- -168: [07:35:08] testTautomerQueries -168: [07:35:08] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -168: [07:35:08] ------------------------------------- -168: [07:35:08] github3881 recursive smarts with rings -205/223 Test #168: substructLibraryTest ................... Passed 9.18 sec -170: ......[07:35:08] +178/223 Test #168: substructLibraryTest ................... Passed 24.06 sec +test 198 + Start 198: pyScaffoldNetwork + +198: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" +198: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +198: Test timeout computed to be: 1500 +192: 375 +192: Enumeration has completed +192: [04:04:36] Tautomer enumeration stopped at 23 tautomers: canceled +179/223 Test #171: testRGroupDecomp ....................... Passed 23.06 sec +test 199 + Start 199: pyScaffoldNetworkPickling + +199: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" +199: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +199: Test timeout computed to be: 1500 +198: ....... +198: ---------------------------------------------------------------------- +198: Ran 7 tests in 0.130s +198: +198: OK +199: . +199: ---------------------------------------------------------------------- +199: Ran 1 test in 0.050s +199: +199: OK +180/223 Test #198: pyScaffoldNetwork ...................... Passed 2.00 sec +test 200 + Start 200: testMolEnumerator + +200: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator +200: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator +200: Test timeout computed to be: 1500 +181/223 Test #199: pyScaffoldNetworkPickling .............. Passed 1.23 sec +test 201 + Start 201: pyMolEnumerator + +201: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" +201: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap +201: Test timeout computed to be: 1500 +200: Randomness seeded to: 1020404510 +200: [04:04:38] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +192: CN=c1cc[nH]cn1 +192: CN=c1ccnc[nH]1 +192: CNc1ccncn1 +192: res: CNc1ccncn1 +192: CN=c1cccc[nH]1 +192: CNc1ccccn1 +192: res: CNc1ccccn1 +200: =============================================================================== +200: All tests passed (321 assertions in 16 test cases) +200: +182/223 Test #200: testMolEnumerator ...................... Passed 0.46 sec +test 202 + Start 202: testAbbreviations + +202: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations +202: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations +202: Test timeout computed to be: 1500 +202: Randomness seeded to: 1219477550 +202: [04:04:38] SMARTS Parse Error: syntax error while parsing: *fail +202: [04:04:38] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +202: [04:04:38] no suitable SubstanceGroups found +202: =============================================================================== +202: All tests passed (195 assertions in 12 test cases) +202: +183/223 Test #202: testAbbreviations ...................... Passed 0.14 sec +test 203 + Start 203: pyAbbreviations + +203: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" +203: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap +203: Test timeout computed to be: 1500 +196: Enumeration has completed +196: [04:04:39] Tautomer enumeration stopped at 37 tautomers: canceled +184/223 Test #192: molTautomerTest ........................ Passed 11.97 sec +test 204 + Start 204: generalizedSubstructCatch + +204: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch +204: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct +204: Test timeout computed to be: 1500 +203: ....... +203: ---------------------------------------------------------------------- +203: Ran 7 tests in 0.092s +203: +203: OK +185/223 Test #203: pyAbbreviations ........................ Passed 1.07 sec +test 205 + Start 205: pyGeneralizedSubstruct + +205: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" +205: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap +205: Test timeout computed to be: 1500 +204: Randomness seeded to: 1720494927 +204: =============================================================================== +204: All tests passed (180 assertions in 10 test cases) +204: +186/223 Test #204: generalizedSubstructCatch .............. Passed 0.80 sec +test 206 + Start 206: testQuery + +206: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Query/testQuery +206: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/Query +206: Test timeout computed to be: 1500 +206: Query +206: Query2 +206: Equality +206: Greater +206: GreaterEqual +206: Less +206: LessEqual +206: Open Range +206: Closed Range +206: Float +206: With Tolerance +206: Set +206: And +206: Or +206: XOr +206: pointer and copy foo +206: Set2 +187/223 Test #206: testQuery .............................. Passed 0.03 sec +test 207 + Start 207: testMatCalc + +207: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc +207: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc +207: Test timeout computed to be: 1500 +207: 1.68022e+08 +207: 1.73149e+08 +207: 1.05549e+08 +207: 7.20603e+07 +207: 1.41535e+08 +207: 1.08592e+08 +207: 1.11334e+08 +207: 2.05553e+08 +207: 1.54962e+08 +207: 8.08231e+07 +207: 5.61421e+07 +207: 1.28874e+08 +207: 1.59011e+08 +207: 8.69902e+07 +207: 1.31367e+08 +207: 2.27389e+08 +207: 1.60289e+08 +207: 7.79813e+07 +207: 1.61001e+08 +207: 2.07599e+08 +207: 2.24432e+08 +207: 1.39725e+08 +207: 2.42614e+08 +207: 1.77578e+08 +207: 1.05908e+08 +207: 9.06742e+07 +207: 1.8087e+08 +207: 1.98182e+08 +207: 2.03052e+08 +207: 1.7673e+08 +207: 9.32798e+07 +207: 1.37969e+08 +207: 1.83778e+08 +207: 2.1228e+08 +207: 5.06157e+07 +207: 1.566e+08 +207: 2.37142e+08 +207: 1.49345e+08 +207: 7.05819e+07 +207: 1.71633e+08 +207: 1.96817e+08 +207: 2.18246e+08 +207: 9.49496e+07 +207: 2.25618e+08 +207: 1.30219e+08 +188/223 Test #207: testMatCalc ............................ Passed 0.01 sec +test 208 + Start 208: pyMatCalc + +208: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" +208: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap +208: Test timeout computed to be: 1500 +201: ... +201: ---------------------------------------------------------------------- +201: Ran 3 tests in 0.107s +201: +201: OK +197: Randomness seeded to: 1013568628 +197: =============================================================================== +197: All tests passed (269 assertions in 19 test cases) +197: +189/223 Test #197: testScaffoldNetwork .................... Passed 4.70 sec +test 209 + Start 209: testSimDivPickers + +209: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/testSimDivPickers +209: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers +209: Test timeout computed to be: 1500 +209: [04:04:40] ------------------------------------- +209: [04:04:40] Testing github issue 1421: MaxMinPicker picking non-existent element. +209: [04:04:40] Done +209: [04:04:40] ------------------------------------- +209: [04:04:40] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +209: [04:04:40] Done +190/223 Test #209: testSimDivPickers ...................... Passed 0.03 sec +test 210 + Start 210: pickersTestsCatch + +210: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/pickersTestsCatch +210: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers +210: Test timeout computed to be: 1500 +210: Randomness seeded to: 4138310972 +210: =============================================================================== +210: All tests passed (21267 assertions in 1 test case) +210: +191/223 Test #201: pyMolEnumerator ........................ Passed 2.39 sec +192/223 Test #210: pickersTestsCatch ...................... Passed 0.25 sec +test 211 + Start 211: pySimDivPickers + +211: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/testPickers.py" +211: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap +211: Test timeout computed to be: 1500 +test 212 + Start 212: pyRanker + +212: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/testRanker.py" +212: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap +212: Test timeout computed to be: 1500 +196: ....................[04:04:40] Explicit valence for atom # 1 O, 3, is greater than permitted +196: . +196: ---------------------------------------------------------------------- +196: Ran 27 tests in 8.505s +196: +196: OK +196: done +139: .............[04:04:40] Molecule does not have explicit Hs. Consider calling AddHs() +170: ......[04:04:40] 170: 170: **** 170: Pre-condition Violation @@ -26146,7 +25630,7 @@ 170: Failed Expression: df_init 170: **** 170: -170: [07:35:08] +170: [04:04:40] 170: 170: **** 170: Pre-condition Violation @@ -26155,192 +25639,681 @@ 170: Failed Expression: df_init 170: **** 170: -223: ................................... +193/223 Test #196: pyMolStandardize ....................... Passed 10.55 sec +test 213 + Start 213: testChemicalFeatures + +213: Test command: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures +213: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures +213: Test timeout computed to be: 1500 +213: ----------------------------------------- +213: Test1 +213: Done +194/223 Test #213: testChemicalFeatures ................... Passed 0.04 sec +test 214 + Start 214: pyFeatures + +214: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap/testFeatures.py" +214: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap +214: Test timeout computed to be: 1500 +139: [04:04:41] Molecule does not have explicit Hs. Consider calling AddHs() +139: [04:04:41] Molecule does not have explicit Hs. Consider calling AddHs() +212: ..[04:04:41] +212: +212: **** +212: Invariant Violation +212: Can't rank more bits than the ensemble size +212: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp +212: Failed Expression: num <= dp_maskBits->getNumOnBits() +212: **** +212: +212: ... +212: ---------------------------------------------------------------------- +212: Ran 5 tests in 0.086s +212: +212: OK +139: [04:04:41] Molecule does not have explicit Hs. Consider calling AddHs() +139: [04:04:41] Molecule does not have explicit Hs. Consider calling AddHs() +139: [04:04:41] Molecule does not have explicit Hs. Consider calling AddHs() +139: [04:04:41] Molecule does not have explicit Hs. Consider calling AddHs() +139: [04:04:41] Molecule does not have explicit Hs. Consider calling AddHs() +139: [04:04:41] Molecule does not have explicit Hs. Consider calling AddHs() +139: [04:04:41] Molecule does not have explicit Hs. Consider calling AddHs() +139: [04:04:41] Molecule does not have explicit Hs. Consider calling AddHs() +208: ..... +208: ---------------------------------------------------------------------- +208: Ran 5 tests in 0.824s +208: +208: OK +205: ....... +205: ---------------------------------------------------------------------- +205: Ran 7 tests in 0.728s +205: +205: OK +211: [04:04:41] the useCache argument is deprecated and ignored +195/223 Test #212: pyRanker ............................... Passed 1.28 sec +test 215 + Start 215: pythonTestDbCLI + +215: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Projects/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/Projects" +215: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/Projects +215: Test timeout computed to be: 1500 +196/223 Test #208: pyMatCalc .............................. Passed 1.87 sec +test 216 + Start 216: pythonTestDirRoot + +216: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit" +216: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit +216: Test timeout computed to be: 1500 +197/223 Test #205: pyGeneralizedSubstruct ................. Passed 2.33 sec +test 217 + Start 217: pythonTestDirML + +217: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/ML/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/ML" +217: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit +217: Test timeout computed to be: 1500 +214: .. +214: ---------------------------------------------------------------------- +214: Ran 2 tests in 0.026s +214: +214: OK +214: Testing ChemicalFeatures Wrapper code: +211: ...[04:04:42] the useCache argument is deprecated and ignored +211: [04:04:42] the useCache argument is deprecated and ignored +211: .[04:04:42] the useCache argument is deprecated and ignored +198/223 Test #214: pyFeatures ............................. Passed 1.65 sec +test 218 + Start 218: pythonTestDirDataStructs + +218: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs" +218: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit +218: Test timeout computed to be: 1500 +195: =============================================================================== +195: All tests passed (18691 assertions in 41 test cases) +195: +199/223 Test #195: molStandardizeCatchTest ................ Passed 14.04 sec +test 219 + Start 219: pythonTestDirDbase + +219: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase" +219: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit +219: Test timeout computed to be: 1500 +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:21: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML import BuildComposite +218: ....... +218: ---------------------------------------------------------------------- +218: Ran 7 tests in 0.067s +218: +218: OK +180: ...........................[04:04:43] unable to set wavy bonds for double bonds: 3 +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:83: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: refCompos = pickle.load(pklF) +219: .. +219: ---------------------------------------------------------------------- +219: Ran 2 tests in 0.203s +219: +219: OK +180: .........[04:04:43] +180: +180: **** +180: Range Error +180: idx +180: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp +180: Failed Expression: 6 < 5 +180: **** +180: +216: ......................... +216: ---------------------------------------------------------------------- +216: Ran 25 tests in 1.719s +216: +216: OK +200/223 Test #216: pythonTestDirRoot ...................... Passed 2.35 sec +test 220 + Start 220: pythonTestDirSimDivFilters + +220: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters" +220: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit +220: Test timeout computed to be: 1500 +219: ........... +219: ---------------------------------------------------------------------- +219: Ran 11 tests in 0.401s +219: +219: OK +219: . +219: ---------------------------------------------------------------------- +219: Ran 1 test in 0.006s +219: +219: OK +218: .................................. +218: ---------------------------------------------------------------------- +218: Ran 34 tests in 0.024s +218: +218: OK +217: ...../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:198: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: refCompos = pickle.load(pklFile) +219: FF......F...... +219: ====================================================================== +219: FAIL: test1Txt (__main__.TestCase.test1Txt) +219: test reading from a text file +219: ---------------------------------------------------------------------- +219: Traceback (most recent call last): +219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 77, in test1Txt +219: self._confirm(tblName, dbName=self.tempDbName) +219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm +219: assert len(res) == len(colHeads), 'bad number of columns' +219: ^^^^^^^^^^^^^^^^^^^^^^^^^ +219: AssertionError: bad number of columns +219: +219: ====================================================================== +219: FAIL: test3Txt (__main__.TestCase.test3Txt) +219: test reading from a text file including null markers +219: ---------------------------------------------------------------------- +219: Traceback (most recent call last): +219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 87, in test3Txt +219: self._confirm(tblName, dbName=self.tempDbName) +219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm +219: assert len(res) == len(colHeads), 'bad number of columns' +219: ^^^^^^^^^^^^^^^^^^^^^^^^^ +219: AssertionError: bad number of columns +219: +219: ====================================================================== +219: FAIL: test_DatabaseToDatabase (__main__.TestCase.test_DatabaseToDatabase) +219: ---------------------------------------------------------------------- +219: Traceback (most recent call last): +219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 219, in test_DatabaseToDatabase +219: self._confirm(tblName, dbName=self.tempDbName, colHeads=['id', 'val']) +219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm +219: assert len(res) == len(colHeads), 'bad number of columns' +219: ^^^^^^^^^^^^^^^^^^^^^^^^^ +219: AssertionError: bad number of columns +219: +219: ---------------------------------------------------------------------- +219: Ran 15 tests in 0.139s +219: +219: FAILED (failures=3) +217: . +217: ---------------------------------------------------------------------- +217: Ran 6 tests in 1.725s +217: +217: OK +211: ....... +211: ---------------------------------------------------------------------- +211: Ran 11 tests in 4.245s +211: +211: OK +201/223 Test #211: pySimDivPickers ........................ Passed 5.49 sec +test 221 + Start 221: pythonTestDirVLib + +221: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/VLib/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/VLib" +221: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit +221: Test timeout computed to be: 1500 +219: ...... +219: ---------------------------------------------------------------------- +219: Ran 6 tests in 0.023s +219: +219: OK +202/223 Test #220: pythonTestDirSimDivFilters ............. Passed 1.93 sec +test 222 + Start 222: pythonTestSping + +222: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/sping" +222: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit +222: Test timeout computed to be: 1500 +219: !!! TEST FAILURE: python UnitTestDbUtils.py {} +203/223 Test #219: pythonTestDirDbase .....................***Failed 3.36 sec +.. +---------------------------------------------------------------------- +Ran 2 tests in 0.203s + +OK +........... +---------------------------------------------------------------------- +Ran 11 tests in 0.401s + +OK +. +---------------------------------------------------------------------- +Ran 1 test in 0.006s + +OK +FF......F...... +====================================================================== +FAIL: test1Txt (__main__.TestCase.test1Txt) +test reading from a text file +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 77, in test1Txt + self._confirm(tblName, dbName=self.tempDbName) + File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm + assert len(res) == len(colHeads), 'bad number of columns' + ^^^^^^^^^^^^^^^^^^^^^^^^^ +AssertionError: bad number of columns + +====================================================================== +FAIL: test3Txt (__main__.TestCase.test3Txt) +test reading from a text file including null markers +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 87, in test3Txt + self._confirm(tblName, dbName=self.tempDbName) + File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm + assert len(res) == len(colHeads), 'bad number of columns' + ^^^^^^^^^^^^^^^^^^^^^^^^^ +AssertionError: bad number of columns + +====================================================================== +FAIL: test_DatabaseToDatabase (__main__.TestCase.test_DatabaseToDatabase) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 219, in test_DatabaseToDatabase + self._confirm(tblName, dbName=self.tempDbName, colHeads=['id', 'val']) + File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm + assert len(res) == len(colHeads), 'bad number of columns' + ^^^^^^^^^^^^^^^^^^^^^^^^^ +AssertionError: bad number of columns + +---------------------------------------------------------------------- +Ran 15 tests in 0.139s + +FAILED (failures=3) +...... +---------------------------------------------------------------------- +Ran 6 tests in 0.023s + +OK +!!! TEST FAILURE: python UnitTestDbUtils.py {} + +test 223 + Start 223: pythonTestDirChem + +223: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Chem" "--buildType" "None" +223: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit/Chem +223: Test timeout computed to be: 1500 +215: [04:04:46] INFO: Reading molecules and constructing molecular database. +215: +215: [04:04:46] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +215: +215: [04:04:46] INFO: Processing 10 molecules +215: +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:20: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML import ScreenComposite +215: [04:04:46] INFO: Generating fingerprints and descriptors: +215: +218: ..... +218: ---------------------------------------------------------------------- +218: Ran 5 tests in 0.235s +218: +218: OK +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:276: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: compos = pickle.load(pklF) +221: ............. +221: ---------------------------------------------------------------------- +221: Ran 13 tests in 0.061s +221: +221: OK +217: ../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:330: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: compos = pickle.load(pklF) +215: [04:04:47] INFO: Finished. +215: +180: ...................[04:04:47] Explicit valence for atom # 1 F, 2, is greater than permitted +180: [04:04:47] Explicit valence for atom # 6 F, 2, is greater than permitted +180: [04:04:47] Can't kekulize mol. Unkekulized atoms: 3 4 5 +217: .......... +217: ---------------------------------------------------------------------- +217: Ran 12 tests in 0.723s +217: +217: OK +218: ....... +218: ---------------------------------------------------------------------- +218: Ran 7 tests in 0.001s +218: +218: OK +180: ...............[04:04:47] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +204/223 Test #218: pythonTestDirDataStructs ............... Passed 5.31 sec +205/223 Test #184: pyTestThreads .......................... Passed 26.13 sec +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML import AnalyzeComposite +221: ........... +221: ---------------------------------------------------------------------- +221: Ran 11 tests in 0.125s +221: +221: OK +223: ....... 223: ---------------------------------------------------------------------- -223: Ran 35 tests in 1.062s +223: Ran 7 tests in 0.522s 223: 223: OK -26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTreeUtils.py:8: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML.DecTree import TreeUtils +206/223 Test #221: pythonTestDirVLib ...................... Passed 2.87 sec +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:31: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: c1 = pickle.load(pklF) 217: . 217: ---------------------------------------------------------------------- -217: Ran 1 test in 0.000s +217: Ran 1 test in 0.090s 217: 217: OK -26: All 191 tests passed -135: ..[07:35:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTree.py:13: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML.DecTree import Tree -223: .... +139: ...[04:04:49] Molecule does not have explicit Hs. Consider calling AddHs() +139: [04:04:49] Molecule does not have explicit Hs. Consider calling AddHs() +139: [04:04:49] Molecule does not have explicit Hs. Consider calling AddHs() +139: [04:04:49] Molecule does not have explicit Hs. Consider calling AddHs() +139: [04:04:49] Molecule does not have explicit Hs. Consider calling AddHs() +222: .. +222: ---------------------------------------------------------------------- +222: Ran 2 tests in 1.071s +222: +222: OK +139: ... +139: ---------------------------------------------------------------------- +139: Ran 19 tests in 52.980s +139: +139: OK +139: Testing MolAlign Wrappers +215: [04:04:49] INFO: Reading molecules and constructing molecular database. +215: +215: [04:04:49] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +215: +215: [04:04:49] INFO: Processing 163 molecules +215: +207/223 Test #139: pyMolAlign ............................. Passed 54.52 sec +215: [04:04:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:49] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +223: ...... 223: ---------------------------------------------------------------------- -223: Ran 4 tests in 0.012s +223: Ran 6 tests in 0.116s 223: 223: OK -217: ...... +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +208/223 Test #222: pythonTestSping ........................ Passed 4.01 sec +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +217: ... 217: ---------------------------------------------------------------------- -217: Ran 6 tests in 0.001s +217: Ran 3 tests in 0.002s 217: 217: OK -26: -26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestXVal.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML.DecTree import CrossValidate, randomtest -84: 0,0 0 -84: 0,1 0 -84: 1,0 0 -84: 1,1 0 -84: 2,0 0 -84: 2,1 0 -206/223 Test #84: testEnumeration ........................ Passed 11.09 sec +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] INFO: done 100 +215: +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:04:50] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +217: ........ +217: ---------------------------------------------------------------------- +217: Ran 8 tests in 0.001s +217: +217: OK +215: [04:04:51] INFO: Generating fingerprints and descriptors: +215: +223: ....[04:04:51] +223: +223: **** +223: Pre-condition Violation +223: valence not defined for atoms not associated with molecules +223: Violation occurred on line 411 in file ./Code/GraphMol/Atom.cpp +223: Failed Expression: dp_mol +223: **** +223: 223: . 223: ---------------------------------------------------------------------- -223: Ran 1 test in 0.009s +223: Ran 5 tests in 0.030s 223: 223: OK -217: .... -217: ---------------------------------------------------------------------- -217: Ran 4 tests in 0.252s -217: -217: OK -223: ....... +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML.Composite import Composite +223: .... 223: ---------------------------------------------------------------------- -223: Ran 7 tests in 0.029s +223: Ran 4 tests in 0.051s 223: 223: OK -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestID3.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML.DecTree import ID3 -217: ...... -217: ---------------------------------------------------------------------- -217: Ran 6 tests in 0.012s -217: -217: OK -139: .............[07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() -223: ... +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML.DecTree.DecTree import DecTreeNode as Node +26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +223: .. 223: ---------------------------------------------------------------------- -223: Ran 3 tests in 0.031s +223: Ran 2 tests in 0.036s 223: 223: OK -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestPrune.py:9: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML.DecTree import ID3, CrossValidate, PruneTree -139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() -139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() -139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() -139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() -139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() -139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() -139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() -139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() -139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() -139: [07:35:09] Molecule does not have explicit Hs. Consider calling AddHs() -217: .. +26: All 191 tests passed +26: done +26: ------------------------------------- +26: Unit tests for all MMFF constraint terms. +26: 10.0003 +26: done +26: ------------------------------------- +26: Unit test for MMFF TorsionConstraint close to 0 degrees. +26: done +26: ------------------------------------- +26: Unit tests for copying MMFF ForceFields. +26: done +26: ------------------------------------- +26: Unit test for MMFF butane scan. +217: .... 217: ---------------------------------------------------------------------- -217: Ran 2 tests in 0.067s +217: Ran 4 tests in 1.814s 217: 217: OK -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestQuantTree.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML.DecTree import BuildQuantTree -217: .......... +150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +150: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds +150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +150: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds +150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +150: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +150: TOTAL Time elapsed 54.31 seconds +223: ...................... +223: ---------------------------------------------------------------------- +223: Ran 22 tests in 0.113s +223: +223: OK +209/223 Test #150: testFMCS ............................... Passed 54.58 sec +26: done +210/223 Test #26: testMMFFForceField ..................... Passed 70.09 sec +217: ..... 217: ---------------------------------------------------------------------- -217: Ran 10 tests in 0.007s +217: Ran 5 tests in 0.011s 217: 217: OK -157: Randomness seeded to: 1495546223 -157: Timed out after 11 seconds. -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestSigTree.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML.DecTree.BuildSigTree import BuildSigTree, _GenerateRandomEnsemble -217: ..... +217: ......... 217: ---------------------------------------------------------------------- -217: Ran 5 tests in 0.040s +217: Ran 9 tests in 0.018s 217: 217: OK -215: [07:35:09] INFO: Finished. -215: -217: .. +223: .....s.................ss +223: ---------------------------------------------------------------------- +223: Ran 25 tests in 0.457s +223: +223: OK (skipped=3) +223: ..s +223: ---------------------------------------------------------------------- +223: Ran 3 tests in 0.285s +223: +223: OK (skipped=1) +217: ............ 217: ---------------------------------------------------------------------- -217: Ran 2 tests in 0.002s +217: Ran 12 tests in 0.007s 217: 217: OK -215: .[07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: ..... 217: ---------------------------------------------------------------------- -217: Ran 5 tests in 0.007s +217: Ran 5 tests in 0.123s 217: 217: OK -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +223: ................................... +223: ---------------------------------------------------------------------- +223: Ran 35 tests in 1.135s +223: +223: OK +223: .... +223: ---------------------------------------------------------------------- +223: Ran 4 tests in 0.048s +223: +223: OK 170: ............. 170: ---------------------------------------------------------------------- -170: Ran 19 tests in 10.958s +170: Ran 19 tests in 47.733s 170: 170: OK 170: Testing atom rings @@ -26348,525 +26321,22 @@ 170: searching atom rings 170: searching bond rings 170: done -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -217: ... +211/223 Test #170: pySubstructLibrary ..................... Passed 49.25 sec +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTreeUtils.py:8: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML.DecTree import TreeUtils +217: . 217: ---------------------------------------------------------------------- -217: Ran 3 tests in 0.007s +217: Ran 1 test in 0.001s 217: 217: OK -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -207/223 Test #170: pySubstructLibrary ..................... Passed 11.41 sec -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -223: .ss.ss....... +215: [04:05:02] INFO: Finished. +215: +223: . 223: ---------------------------------------------------------------------- -223: Ran 13 tests in 1.010s +223: Ran 1 test in 0.052s 223: -223: OK (skipped=4) -217: ... -217: ---------------------------------------------------------------------- -217: Ran 3 tests in 0.181s -217: -217: OK -223: [07:35:10] Molecule does not have explicit Hs. Consider calling AddHs() -223: .[07:35:10] Molecule does not have explicit Hs. Consider calling AddHs() -215: .[07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:10] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/KNN/UnitTestKNN.py:11: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML.KNN import (CrossValidate, DistFunctions, KNNModel, -1: terminate called after throwing an instance of 'Invar::Invariant' -1: what(): Expression Failed: -208/223 Test #1: testInchi ..............................Subprocess aborted***Exception: 13.78 sec -[07:34:57] ------------------------------------- -[07:34:57] ------------------------------------- -[07:34:57] ------------------------------------- -[07:34:57] ------------------------------------- -[07:34:57] Extended double-bond stereochemistry (e.g. C=C=C=C) ignored -[07:34:57] ------------------------------------- -[07:34:57] ------------------------------------- -[07:34:57] ------------------------------------- -[07:34:57] Test multithreading -reading molecules -generating reference data -processing - launch :0 - launch :1 - launch :2 - launch :3 -[07:34:57] - -**** -Test Assert -Expression Failed: -Violation occurred on line 41 in file ./External/INCHI-API/test.cpp -Failed Expression: inchi == inchis[i] -**** - -[07:34:57] Invalid InChI prefix in generating InChI Key -[07:34:57] - -**** -Test Assert -Expression Failed: -Violation occurred on line 45 in file ./External/INCHI-API/test.cpp -Failed Expression: key2 == keys[i] -**** - -[07:34:57] - -**** -Test Assert -Expression Failed: -Violation occurred on line 41 in file ./External/INCHI-API/test.cpp -Failed Expression: inchi == inchis[i] -**** - -terminate called after throwing an instance of 'Invar::Invariant' - what(): Expression Failed: - -217: ...... -217: ---------------------------------------------------------------------- -217: Ran 6 tests in 0.172s -217: -217: OK -215: .[07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -139: ...[07:35:11] Molecule does not have explicit Hs. Consider calling AddHs() -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML.Composite import Composite -139: [07:35:11] Molecule does not have explicit Hs. Consider calling AddHs() -139: [07:35:11] Molecule does not have explicit Hs. Consider calling AddHs() -139: [07:35:11] Molecule does not have explicit Hs. Consider calling AddHs() -139: [07:35:11] Molecule does not have explicit Hs. Consider calling AddHs() -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML.ModelPackage import Packager, PackageUtils -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:72: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: model = pickle.load(modelF) -26: All 191 tests passed -26: done -26: ------------------------------------- -26: Unit tests for all MMFF constraint terms. -26: 10.0003 -26: done -26: ------------------------------------- -26: Unit test for MMFF TorsionConstraint close to 0 degrees. -26: done -26: ------------------------------------- -26: Unit tests for copying MMFF ForceFields. -26: done -26: ------------------------------------- -26: Unit test for MMFF butane scan. -180: ..[07:35:11] +223: OK +180: ..[04:05:02] 180: 180: **** 180: Pre-condition Violation @@ -26875,7 +26345,7 @@ 180: Failed Expression: dp_mol 180: **** 180: -180: [07:35:11] +180: [04:05:02] 180: 180: **** 180: Pre-condition Violation @@ -26884,7 +26354,7 @@ 180: Failed Expression: dp_mol 180: **** 180: -180: [07:35:11] +180: [04:05:02] 180: 180: **** 180: Pre-condition Violation @@ -26893,7 +26363,7 @@ 180: Failed Expression: dp_mol 180: **** 180: -180: [07:35:11] +180: [04:05:02] 180: 180: **** 180: Pre-condition Violation @@ -26902,7 +26372,7 @@ 180: Failed Expression: dp_mol 180: **** 180: -180: [07:35:11] +180: [04:05:02] 180: 180: **** 180: Pre-condition Violation @@ -26911,13 +26381,7 @@ 180: Failed Expression: dp_mol 180: **** 180: -139: ... -139: ---------------------------------------------------------------------- -139: Ran 19 tests in 13.088s -139: -139: OK -139: Testing MolAlign Wrappers -180: .....[07:35:11] +180: .....[04:05:02] 180: 180: **** 180: Range Error @@ -26926,40 +26390,49 @@ 180: Failed Expression: 0 < 0 180: **** 180: -217: ....... +137: --------------------------------- +137: test O3A multithreading bug +137: +137: --------------------------------- +137: testCrippenO3A multithreading +137: +137: generating reference data +180: ......[04:05:02] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +180: [04:05:02] ERROR: Smiles parse error on line 0 +180: [04:05:02] ERROR: Cannot create molecule from : 'c1ccccc' +180: [04:05:02] SMILES Parse Error: extra open parentheses for input: 'C(C' +180: [04:05:02] ERROR: Smiles parse error on line 3 +180: [04:05:02] ERROR: Cannot create molecule from : 'C(C' +180: [04:05:02] Explicit valence for atom # 1 C, 5, is greater than permitted +180: [04:05:02] ERROR: Could not sanitize molecule on line 6 +180: [04:05:02] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +180: [04:05:02] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +180: [04:05:02] ERROR: Smiles parse error on line 0 +180: [04:05:02] ERROR: Cannot create molecule from : 'c1ccccc' +180: [04:05:02] SMILES Parse Error: extra open parentheses for input: 'C(C' +180: [04:05:02] ERROR: Smiles parse error on line 3 +180: [04:05:02] ERROR: Cannot create molecule from : 'C(C' +180: [04:05:02] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +180: [04:05:02] ERROR: Smiles parse error on line 6 +180: [04:05:02] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +180: [04:05:02] Explicit valence for atom # 1 F, 2, is greater than permitted +180: [04:05:02] ERROR: Could not sanitize molecule ending on line 21 +180: [04:05:02] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +180: [04:05:02] ERROR: EOF hit while reading atoms +180: [04:05:02] ERROR: moving to the beginning of the next molecule +180: [04:05:02] Explicit valence for atom # 1 F, 2, is greater than permitted +180: [04:05:02] ERROR: Could not sanitize molecule ending on line 21 +180: [04:05:02] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +180: [04:05:02] ERROR: EOF hit while reading atoms +180: [04:05:02] ERROR: moving to the beginning of the next molecule +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTree.py:13: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML.DecTree import Tree +217: ...... 217: ---------------------------------------------------------------------- -217: Ran 7 tests in 0.079s +217: Ran 6 tests in 0.005s 217: 217: OK -180: ......[07:35:11] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -180: [07:35:11] ERROR: Smiles parse error on line 0 -180: [07:35:11] ERROR: Cannot create molecule from : 'c1ccccc' -180: [07:35:11] SMILES Parse Error: extra open parentheses for input: 'C(C' -180: [07:35:11] ERROR: Smiles parse error on line 3 -180: [07:35:11] ERROR: Cannot create molecule from : 'C(C' -180: [07:35:11] Explicit valence for atom # 1 C, 5, is greater than permitted -180: [07:35:11] ERROR: Could not sanitize molecule on line 6 -180: [07:35:11] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -180: [07:35:11] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -180: [07:35:11] ERROR: Smiles parse error on line 0 -180: [07:35:11] ERROR: Cannot create molecule from : 'c1ccccc' -180: [07:35:11] SMILES Parse Error: extra open parentheses for input: 'C(C' -180: [07:35:11] ERROR: Smiles parse error on line 3 -180: [07:35:11] ERROR: Cannot create molecule from : 'C(C' -180: [07:35:11] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -180: [07:35:11] ERROR: Smiles parse error on line 6 -180: [07:35:11] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -180: [07:35:11] Explicit valence for atom # 1 F, 2, is greater than permitted -180: [07:35:11] ERROR: Could not sanitize molecule ending on line 21 -180: [07:35:11] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -180: [07:35:11] ERROR: EOF hit while reading atoms -180: [07:35:11] ERROR: moving to the beginning of the next molecule -180: [07:35:11] Explicit valence for atom # 1 F, 2, is greater than permitted -180: [07:35:11] ERROR: Could not sanitize molecule ending on line 21 -180: [07:35:11] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -180: [07:35:11] ERROR: EOF hit while reading atoms -180: [07:35:11] ERROR: moving to the beginning of the next molecule -180: ....[07:35:11] +180: ....[04:05:02] 180: 180: **** 180: Pre-condition Violation @@ -26968,7 +26441,7 @@ 180: Failed Expression: df_init 180: **** 180: -180: ..........[07:35:11] +180: ..........[04:05:02] 180: 180: **** 180: Range Error @@ -26977,777 +26450,1340 @@ 180: Failed Expression: 3 < 1 180: **** 180: -180: ..[07:35:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -209/223 Test #139: pyMolAlign ............................. Passed 13.46 sec -180: ..........................[07:35:11] SMILES Parse Error: unclosed ring for input: 'C1CC' -180: ......[07:35:11] WARNING: not removing hydrogen atom without neighbors -180: [07:35:11] WARNING: not removing hydrogen atom with dummy atom neighbors -180: [07:35:11] WARNING: not removing hydrogen atom with wedged bond -180: [07:35:11] WARNING: not removing hydrogen atom without neighbors -180: [07:35:11] WARNING: not removing hydrogen atom with dummy atom neighbors -26: done -210/223 Test #26: testMMFFForceField ..................... Passed 14.49 sec -180: .....[07:35:11] Explicit valence for atom # 1 F, 2, is greater than permitted -180: [07:35:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 -180: .[07:35:11] Explicit valence for atom # 1 F, 2, is greater than permitted -180: [07:35:11] Explicit valence for atom # 1 F, 2, is greater than permitted -180: [07:35:11] Explicit valence for atom # 1 F, 2, is greater than permitted -180: [07:35:11] Explicit valence for atom # 1 F, 2, is greater than permitted -180: [07:35:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 -180: [07:35:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 -180: [07:35:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 -217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/NaiveBayes/UnitTestNB.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -217: from rdkit.ML.NaiveBayes import CrossValidate -180: ..........[07:35:11] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -180: [07:35:11] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -180: .[07:35:11] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -180: [07:35:11] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -180: ..[07:35:11] SMILES Parse Error: syntax error while parsing: error -180: [07:35:11] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -180: [07:35:11] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -180: [07:35:11] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -180: [07:35:11] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -217: .... -217: ---------------------------------------------------------------------- -217: Ran 4 tests in 0.006s -217: -217: OK -180: ................[07:35:12] SMILES Parse Error: syntax error while parsing: garbage_0 -180: [07:35:12] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -180: [07:35:12] SMILES Parse Error: syntax error while parsing: garbage_2 -180: [07:35:12] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -180: [07:35:12] SMILES Parse Error: syntax error while parsing: garbage_4 -180: [07:35:12] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +180: ..[04:05:02] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestXVal.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML.DecTree import CrossValidate, randomtest +180: ..........................[04:05:03] SMILES Parse Error: unclosed ring for input: 'C1CC' +180: ......[04:05:03] WARNING: not removing hydrogen atom without neighbors +180: [04:05:03] WARNING: not removing hydrogen atom with dummy atom neighbors +180: [04:05:03] WARNING: not removing hydrogen atom with wedged bond +180: [04:05:03] WARNING: not removing hydrogen atom without neighbors +180: [04:05:03] WARNING: not removing hydrogen atom with dummy atom neighbors +223: ....... +223: ---------------------------------------------------------------------- +223: Ran 7 tests in 0.159s +223: +223: OK +180: .....[04:05:04] Explicit valence for atom # 1 F, 2, is greater than permitted +180: [04:05:04] Can't kekulize mol. Unkekulized atoms: 0 1 2 +180: .[04:05:04] Explicit valence for atom # 1 F, 2, is greater than permitted +180: [04:05:04] Explicit valence for atom # 1 F, 2, is greater than permitted +180: [04:05:04] Explicit valence for atom # 1 F, 2, is greater than permitted +180: [04:05:04] Explicit valence for atom # 1 F, 2, is greater than permitted +180: [04:05:04] Can't kekulize mol. Unkekulized atoms: 0 1 2 +180: [04:05:04] Can't kekulize mol. Unkekulized atoms: 0 1 2 +180: [04:05:04] Can't kekulize mol. Unkekulized atoms: 0 1 2 +215: .[04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +180: ..........[04:05:04] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +180: [04:05:04] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +180: .[04:05:04] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +180: [04:05:04] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +180: ..[04:05:04] SMILES Parse Error: syntax error while parsing: error +180: [04:05:04] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +180: [04:05:04] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +180: [04:05:04] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +180: [04:05:04] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +180: ................[04:05:04] SMILES Parse Error: syntax error while parsing: garbage_0 +180: [04:05:04] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +180: [04:05:04] SMILES Parse Error: syntax error while parsing: garbage_2 +180: [04:05:04] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +180: [04:05:04] SMILES Parse Error: syntax error while parsing: garbage_4 +180: [04:05:04] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 180: .......... 180: ---------------------------------------------------------------------- -180: Ran 248 tests in 11.711s +180: Ran 248 tests in 42.814s 180: 180: OK -180: 643 +180: 1 180: supplier: 180: supplier: 180: supplier: -211/223 Test #180: pyGraphMolWrap ......................... Passed 12.51 sec +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +137: processing +137: launch :0 +137: launch :1 +137: launch :2 +137: launch :3 +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +212/223 Test #180: pyGraphMolWrap ......................... Passed 45.96 sec +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +223: ... +223: ---------------------------------------------------------------------- +223: Ran 3 tests in 0.212s +223: +223: OK +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +217: .... +217: ---------------------------------------------------------------------- +217: Ran 4 tests in 1.957s +217: +217: OK +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestID3.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML.DecTree import ID3 +217: ...... +217: ---------------------------------------------------------------------- +217: Ran 6 tests in 0.075s +217: +217: OK +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestPrune.py:9: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML.DecTree import ID3, CrossValidate, PruneTree +215: .[04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +217: .. +217: ---------------------------------------------------------------------- +217: Ran 2 tests in 0.325s +217: +217: OK +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestQuantTree.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML.DecTree import BuildQuantTree +217: .......... +217: ---------------------------------------------------------------------- +217: Ran 10 tests in 0.014s +217: +217: OK +223: .ss.ss....... +223: ---------------------------------------------------------------------- +223: Ran 13 tests in 2.145s +223: +223: OK (skipped=4) +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestSigTree.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML.DecTree.BuildSigTree import BuildSigTree, _GenerateRandomEnsemble +217: ..... +217: ---------------------------------------------------------------------- +217: Ran 5 tests in 0.091s +217: +217: OK +215: .[04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +223: [04:05:09] Molecule does not have explicit Hs. Consider calling AddHs() +223: .[04:05:09] Molecule does not have explicit Hs. Consider calling AddHs() +217: .. +217: ---------------------------------------------------------------------- +217: Ran 2 tests in 0.015s +217: +217: OK +217: ..... +217: ---------------------------------------------------------------------- +217: Ran 5 tests in 0.048s +217: +217: OK +217: ... +217: ---------------------------------------------------------------------- +217: Ran 3 tests in 0.052s +217: +217: OK +135: ......[04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: .[04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: .[04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: [04:05:12] Molecule does not have explicit Hs. Consider calling AddHs() +135: . +135: ---------------------------------------------------------------------- +135: Ran 19 tests in 76.782s +135: +135: OK +213/223 Test #135: pyDistGeomHelpers ...................... Passed 78.56 sec +217: ... +217: ---------------------------------------------------------------------- +217: Ran 3 tests in 1.008s +217: +217: OK +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/KNN/UnitTestKNN.py:11: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML.KNN import (CrossValidate, DistFunctions, KNNModel, +215: ....[04:05:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +217: ...... +217: ---------------------------------------------------------------------- +217: Ran 6 tests in 0.620s +217: +217: OK +215: [04:05:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML.Composite import Composite +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML.ModelPackage import Packager, PackageUtils +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:72: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: model = pickle.load(modelF) +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +217: ....... +217: ---------------------------------------------------------------------- +217: Ran 7 tests in 0.467s +217: +217: OK +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/NaiveBayes/UnitTestNB.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +217: from rdkit.ML.NaiveBayes import CrossValidate +217: .... +217: ---------------------------------------------------------------------- +217: Ran 4 tests in 0.034s +217: +217: OK +215: [04:05:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestTrainer.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.Neural import Network, Trainers -137: --------------------------------- -137: test O3A multithreading bug -137: -137: --------------------------------- -137: testCrippenO3A multithreading -137: -137: generating reference data -215: ....[07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:23] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +157: Timed out after 71 seconds. 217: ..... 217: ---------------------------------------------------------------------- -217: Ran 5 tests in 1.062s +217: Ran 5 tests in 7.470s 217: 217: OK -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -137: processing -137: launch :0 -137: launch :1 -137: launch :2 -137: launch :3 -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestOther.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.Neural.ActFuncs import Sigmoid, TanH -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: .... 217: ---------------------------------------------------------------------- -217: Ran 4 tests in 0.001s +217: Ran 4 tests in 0.007s 217: 217: OK -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: .[04:05:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: .... 217: ---------------------------------------------------------------------- -217: Ran 4 tests in 0.000s +217: Ran 4 tests in 0.001s 217: 217: OK -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -150: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds -150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -150: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds -150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -150: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -150: TOTAL Time elapsed 15.29 seconds -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -212/223 Test #150: testFMCS ............................... Passed 15.33 sec -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 217: .... 217: ---------------------------------------------------------------------- -217: Ran 4 tests in 0.003s +217: Ran 4 tests in 0.006s 217: 217: OK -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -213/223 Test #217: pythonTestDirML ........................ Passed 11.97 sec -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: .[07:35:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: .[07:35:15] INFO: Reading molecules and constructing molecular database. +214/223 Test #217: pythonTestDirML ........................ Passed 49.56 sec +215: .[04:05:33] INFO: Reading molecules and constructing molecular database. 215: -215: [07:35:15] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +215: [04:05:33] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: -215: [07:35:15] INFO: Processing 10 molecules +215: [04:05:33] INFO: Processing 10 molecules 215: -215: [07:35:15] INFO: Generating fingerprints and descriptors: +215: [04:05:33] INFO: Generating fingerprints and descriptors: 215: -215: [07:35:15] INFO: Finished. +215: [04:05:33] INFO: Finished. 215: -215: [07:35:15] INFO: Reading molecules and constructing molecular database. +215: [04:05:38] INFO: Reading molecules and constructing molecular database. 215: -215: [07:35:15] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +215: [04:05:38] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: -215: [07:35:15] INFO: Processing 10 molecules +215: [04:05:38] INFO: Processing 10 molecules 215: -215: [07:35:15] INFO: Generating fingerprints and descriptors: +215: [04:05:38] INFO: Generating fingerprints and descriptors: 215: -215: [07:35:15] INFO: Finished. +215: [04:05:38] INFO: Finished. 215: -135: ......[07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: .[07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: .[07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: [07:35:16] Molecule does not have explicit Hs. Consider calling AddHs() -135: . -135: ---------------------------------------------------------------------- -135: Ran 19 tests in 17.784s -135: -135: OK -214/223 Test #135: pyDistGeomHelpers ...................... Passed 18.17 sec -215: [07:35:16] INFO: Reading molecules and constructing molecular database. +215: [04:05:42] INFO: Reading molecules and constructing molecular database. 215: -215: [07:35:16] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +215: [04:05:42] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: -215: [07:35:16] INFO: Processing 10 molecules +215: [04:05:42] INFO: Processing 10 molecules 215: -215: [07:35:16] INFO: Generating fingerprints and descriptors: +215: [04:05:42] INFO: Generating fingerprints and descriptors: 215: -215: [07:35:16] INFO: Finished. +215: [04:05:42] INFO: Finished. 215: -215: [07:35:17] INFO: Reading molecules and constructing molecular database. +215: [04:05:47] INFO: Reading molecules and constructing molecular database. 215: -215: [07:35:17] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +215: [04:05:47] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: -215: [07:35:17] INFO: Generating fingerprints and descriptors: +215: [04:05:47] INFO: Generating fingerprints and descriptors: 215: -215: [07:35:17] INFO: Finished. +215: [04:05:47] INFO: Finished. 215: -215: [07:35:17] INFO: Reading molecules and constructing molecular database. +137: --------------------------------- +137: test getO3AForProbeConfs +137: +137: *********************************************************** +215/223 Test #137: testO3AAlign ........................... Passed 116.58 sec +215: [04:05:51] INFO: Reading molecules and constructing molecular database. 215: -215: [07:35:17] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +215: [04:05:51] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: -215: [07:35:17] INFO: Generating fingerprints and descriptors: +215: [04:05:52] INFO: Generating fingerprints and descriptors: 215: -215: [07:35:17] INFO: Finished. +215: [04:05:52] INFO: Finished. 215: -215: .[07:35:18] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. +215: .[04:05:55] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. 215: -215: [07:35:18] INFO: Reading molecules and constructing molecular database. +215: [04:05:55] INFO: Reading molecules and constructing molecular database. 215: -215: [07:35:18] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +215: [04:05:55] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: -215: [07:35:18] INFO: Processing 163 molecules +215: [04:05:55] INFO: Processing 163 molecules 215: -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] INFO: done 100 +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] INFO: done 100 215: -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] INFO: Generating fingerprints and descriptors: +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:05:56] INFO: Generating fingerprints and descriptors: 215: -215: [07:35:18] INFO: Finished. +215: [04:05:58] INFO: Finished. 215: -30: [07:35:18] Finished -30: [07:35:18] ------------------------------------- -30: [07:35:18] Test github1843: RWMol.clear() should not destroy ring pointer. -30: [07:35:18] Finished -215/223 Test #30: graphmolTest1 .......................... Passed 21.46 sec -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -6: [07:35:19] Finished: testMultipleTimes() -6: [07:35:19] -6: ----------------------------------------- -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -216/223 Test #6: testConcurrentQueue .................... Passed 21.69 sec -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -215: [07:35:19] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -137: --------------------------------- -137: test getO3AForProbeConfs -137: -137: *********************************************************** -217/223 Test #137: testO3AAlign ........................... Passed 21.12 sec -215: .[07:35:19] INFO: Reading molecules and constructing molecular database. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: [04:06:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +215: .[04:06:05] INFO: Reading molecules and constructing molecular database. 215: -215: [07:35:19] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +215: [04:06:05] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: -215: [07:35:19] INFO: Processing 10 molecules +215: [04:06:05] INFO: Processing 10 molecules 215: -215: [07:35:19] INFO: Generating fingerprints and descriptors: +215: [04:06:07] INFO: Generating fingerprints and descriptors: 215: -215: [07:35:19] INFO: Finished. +215: [04:06:07] INFO: Finished. 215: -215: [07:35:20] INFO: Reading molecules and constructing molecular database. +215: [04:06:11] INFO: Reading molecules and constructing molecular database. 215: -215: [07:35:20] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +215: [04:06:11] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 215: -215: [07:35:20] INFO: Processing 10 molecules +215: [04:06:11] INFO: Processing 10 molecules 215: -215: [07:35:21] INFO: Generating fingerprints and descriptors: +215: [04:06:12] INFO: Generating fingerprints and descriptors: 215: -215: [07:35:21] INFO: Finished. +215: [04:06:13] INFO: Finished. 215: 215: . 215: ---------------------------------------------------------------------- -215: Ran 12 tests in 19.424s +215: Ran 12 tests in 90.787s 215: 215: OK -218/223 Test #215: pythonTestDbCLI ........................ Passed 19.77 sec -134: [07:35:34] UFFTYPER: Unrecognized atom type: S_6+6 (0) -134: [07:35:34] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -134: [07:35:34] UFFTYPER: Unrecognized charge state for atom: 0 +216/223 Test #215: pythonTestDbCLI ........................ Passed 92.12 sec +134: [04:06:32] UFFTYPER: Unrecognized atom type: S_6+6 (0) +134: [04:06:32] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +134: [04:06:32] UFFTYPER: Unrecognized charge state for atom: 0 134: =============================================================================== 134: All tests passed (448 assertions in 10 test cases) 134: -219/223 Test #134: distGeomHelpersCatch ................... Passed 36.55 sec -223: ....................[07:35:37] WARNING: More than one matching pattern found - picking one -223: -223: [07:35:37] WARNING: More than one matching pattern found - picking one -223: -223: .[07:35:37] WARNING: More than one matching pattern found - picking one -223: +217/223 Test #134: distGeomHelpersCatch ................... Passed 160.50 sec 158: =============================================================================== 158: All tests passed (93 assertions in 5 test cases) 158: -220/223 Test #158: testRascalCluster ...................... Passed 40.50 sec +218/223 Test #158: testRascalCluster ...................... Passed 150.39 sec +157: =============================================================================== +157: All tests passed (2552 assertions in 23 test cases) +157: +219/223 Test #157: testRascalMCES ......................... Passed 174.84 sec +223: ....................[04:07:01] WARNING: More than one matching pattern found - picking one +223: +223: [04:07:01] WARNING: More than one matching pattern found - picking one +223: +223: .[04:07:01] WARNING: More than one matching pattern found - picking one +223: +30: [04:07:10] Finished +30: [04:07:10] ------------------------------------- +30: [04:07:10] Test github1843: RWMol.clear() should not destroy ring pointer. +30: [04:07:10] Finished +220/223 Test #30: graphmolTest1 .......................... Passed 205.53 sec 223: ... 223: ---------------------------------------------------------------------- -223: Ran 25 tests in 30.624s +223: Ran 25 tests in 125.061s 223: 223: OK -223: {'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl'} -223: {'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl'} -223: {'F[C@H](Cl)[C@@H](F)Cl', 'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@H](F)Cl'} +223: {'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl'} +223: {'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl'} +223: {'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@H](F)Cl'} 223: !!!! ['C[C@H]([C@H](C)Br)[C@@H](C)F', 'C[C@@H]([C@@H](C)F)[C@@H](C)Br', 'C[C@@H]([C@H](C)Br)[C@@H](C)F', 'C[C@H]([C@@H](C)F)[C@@H](C)Br', 'C[C@@H]([C@H](C)F)[C@H](C)Br', 'C[C@@H]([C@H](C)F)[C@@H](C)Br', 'C[C@H]([C@H](C)F)[C@H](C)Br', 'C[C@H]([C@H](C)F)[C@@H](C)Br'] 223: ........ 223: ---------------------------------------------------------------------- -223: Ran 8 tests in 0.136s +223: Ran 8 tests in 0.168s 223: 223: OK -223: .[07:35:42] Molecule does not have explicit Hs. Consider calling AddHs() -223: .....[07:35:46] WARNING: not removing hydrogen atom without neighbors -223: [07:35:46] WARNING: not removing hydrogen atom without neighbors -223: [07:35:46] WARNING: not removing hydrogen atom without neighbors -223: ....[07:35:46] WARNING: not removing hydrogen atom without neighbors +223: .[04:07:16] Molecule does not have explicit Hs. Consider calling AddHs() +223: .....[04:07:25] WARNING: not removing hydrogen atom without neighbors +223: [04:07:25] WARNING: not removing hydrogen atom without neighbors +223: [04:07:25] WARNING: not removing hydrogen atom without neighbors +223: ....[04:07:25] WARNING: not removing hydrogen atom without neighbors 223: ...... 223: ---------------------------------------------------------------------- -223: Ran 16 tests in 3.589s +223: Ran 16 tests in 8.580s 223: 223: OK -223: [07:35:46] WARNING: Omitted undefined stereo +133: [04:07:25] done +223: [04:07:26] WARNING: Omitted undefined stereo 223: -223: [07:35:46] WARNING: Proton(s) added/removed +223: [04:07:26] WARNING: Proton(s) added/removed 223: -223: ..[07:35:48] ERROR: Add/Remove protons error; *Conversion failed* +223: ..[04:07:29] ERROR: Add/Remove protons error; *Conversion failed* 223: -223: [07:35:48] ERROR: Add/Remove protons error; *Conversion failed* +223: [04:07:29] ERROR: Add/Remove protons error; *Conversion failed* 223: 223: E.... 223: ====================================================================== @@ -27760,19 +27796,20 @@ 223: AttributeError: 'NoneType' object has no attribute 'GetAtoms' 223: 223: ---------------------------------------------------------------------- -223: Ran 7 tests in 2.440s +223: Ran 7 tests in 3.547s 223: 223: FAILED (errors=1) 223: 223: InChI write Summary: 1160 identical, 0 suffix variance, 21 reasonable 223: .... 223: ---------------------------------------------------------------------- -223: Ran 4 tests in 1.448s +223: Ran 4 tests in 4.878s 223: 223: OK +133: CNC[C@H]1CC[C@H](C[NH3+])CC1 223: ...... 223: ---------------------------------------------------------------------- -223: Ran 6 tests in 0.347s +223: Ran 6 tests in 0.647s 223: 223: OK 223: /build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestPandasTools.py:218: SyntaxWarning: invalid escape sequence '\O' @@ -27787,7 +27824,10 @@ 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering +133: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 223: Failed to patch pandas - unable to change molecule rendering +133: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 +133: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 223: Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering @@ -27800,7 +27840,6 @@ 223: Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering -133: [07:35:53] done 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: Failed to patch pandas - unable to change molecule rendering @@ -27810,6 +27849,7 @@ 223: FFailed to patch pandas - unable to change molecule rendering 223: .sFailed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering +133: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 223: .sFailed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering 223: .Failed to patch pandas - unable to change molecule rendering @@ -27826,7 +27866,7 @@ 223: Traceback (most recent call last): 223: File "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestPandasTools.py", line 229, in testPandasShouldShowMoleculesWhenTruncating 223: self.assertIn('data-content="rdkit/molecule"', html_output) -223: AssertionError: 'data-content="rdkit/molecule"' not found in '
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
Molecule ChEMBL IDMolecule NameMolecule Max PhaseMolecular Weight#RO5 Violations...Source DescriptionDocument JournalDocument YearCell ChEMBL IDROMol
0"CHEMBL543779"NaN0341.860...Scientific LiteratureJ. Med. Chem.1986NaN<rdkit.Chem.rdchem.Mol object at 0x7f875127b060>
\n
' +223: AssertionError: 'data-content="rdkit/molecule"' not found in '
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
Molecule ChEMBL IDMolecule NameMolecule Max PhaseMolecular Weight#RO5 Violations...Source DescriptionDocument JournalDocument YearCell ChEMBL IDROMol
0"CHEMBL543779"NaN0341.860...Scientific LiteratureJ. Med. Chem.1986NaN<rdkit.Chem.rdchem.Mol object at 0x7f963fbd6f80>
\n
' 223: 223: ====================================================================== 223: FAIL: test_RestoreMonkeyPatch (__main__.TestPandasTools.test_RestoreMonkeyPatch) @@ -27834,341 +27874,334 @@ 223: Traceback (most recent call last): 223: File "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestPandasTools.py", line 64, in test_RestoreMonkeyPatch 223: self.assertIn('data:image/png;base64', html) -223: AssertionError: 'data:image/png;base64' not found in '\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
prop1prop2IDROMolprop3
012.34qweMethane<rdkit.Chem.rdchem.Mol object at 0x7f875127a180>NaN
1NaNrtzPeroxide<rdkit.Chem.rdchem.Mol object at 0x7f87508ba1f0>yxcv
' +223: AssertionError: 'data:image/png;base64' not found in '\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
prop1prop2IDROMolprop3
012.34qweMethane<rdkit.Chem.rdchem.Mol object at 0x7f963fbd6420>NaN
1NaNrtzPeroxide<rdkit.Chem.rdchem.Mol object at 0x7f963f1fa180>yxcv
' 223: 223: ---------------------------------------------------------------------- -223: Ran 28 tests in 1.100s +223: Ran 28 tests in 5.075s 223: 223: FAILED (failures=2, skipped=2) -133: CNC[C@H]1CC[C@H](C[NH3+])CC1 -133: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 -133: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 -133: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 -133: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 133: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O 133: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 133: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 133: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 133: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC -223: ..............[07:36:03] WARNING: More than one matching pattern found - picking one +133: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O +133: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 +133: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 +133: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 +133: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 +133: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 +133: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O +223: ..............[04:08:16] WARNING: More than one matching pattern found - picking one 223: -223: [07:36:03] WARNING: More than one matching pattern found - picking one +223: [04:08:16] WARNING: More than one matching pattern found - picking one 223: -223: ..[07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() -223: [07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() -223: [07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() -223: [07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() +223: ..[04:08:16] Molecule does not have explicit Hs. Consider calling AddHs() +223: [04:08:16] Molecule does not have explicit Hs. Consider calling AddHs() +223: [04:08:16] Molecule does not have explicit Hs. Consider calling AddHs() +223: [04:08:16] Molecule does not have explicit Hs. Consider calling AddHs() 223: ......... 223: ---------------------------------------------------------------------- -223: Ran 25 tests in 9.426s +223: Ran 25 tests in 26.695s 223: 223: OK +133: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O 223: .. 223: ---------------------------------------------------------------------- -223: Ran 2 tests in 0.054s +223: Ran 2 tests in 0.103s 223: 223: OK -133: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O -157: =============================================================================== -157: All tests passed (2552 assertions in 23 test cases) -157: -221/223 Test #157: testRascalMCES ......................... Passed 65.85 sec +133: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 223: ..s... 223: ---------------------------------------------------------------------- -223: Ran 6 tests in 1.017s +223: Ran 6 tests in 2.236s 223: 223: OK (skipped=1) +133: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 223: .. 223: ---------------------------------------------------------------------- -223: Ran 2 tests in 0.017s -223: -223: OK -133: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 -133: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 -133: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 -133: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 -133: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 -133: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O -223: .............. -223: ---------------------------------------------------------------------- -223: Ran 14 tests in 2.605s +223: Ran 2 tests in 0.070s 223: 223: OK -133: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O -133: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O -133: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 133: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 133: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 133: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 133: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 133: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 +223: .............. +223: ---------------------------------------------------------------------- +223: Ran 14 tests in 10.781s +223: +223: OK 133: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 133: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 -223: ..[07:36:18] WARNING: not removing hydrogen atom without neighbors -223: .[07:36:18] WARNING: not removing hydrogen atom without neighbors -223: .[07:36:18] WARNING: no name column found on line 1 -223: [07:36:18] WARNING: no name column found on line 2 -223: [07:36:18] WARNING: no name column found on line 3 -223: [07:36:18] WARNING: no name column found on line 4 -223: [07:36:18] WARNING: no name column found on line 5 -223: [07:36:18] WARNING: no name column found on line 6 -223: [07:36:18] WARNING: no name column found on line 7 -223: [07:36:18] WARNING: no name column found on line 8 -223: [07:36:18] WARNING: no name column found on line 9 -223: [07:36:18] WARNING: no name column found on line 10 -223: [07:36:18] WARNING: no name column found on line 11 -223: [07:36:18] WARNING: no name column found on line 12 -223: [07:36:18] WARNING: no name column found on line 13 -223: [07:36:18] WARNING: no name column found on line 14 -223: [07:36:18] WARNING: no name column found on line 15 -223: [07:36:18] WARNING: no name column found on line 16 -223: [07:36:18] WARNING: no name column found on line 17 -223: [07:36:18] WARNING: no name column found on line 18 -223: [07:36:18] WARNING: no name column found on line 19 -223: [07:36:18] WARNING: no name column found on line 20 -223: [07:36:18] WARNING: no name column found on line 21 -223: [07:36:18] WARNING: no name column found on line 22 -223: [07:36:18] WARNING: no name column found on line 23 -223: [07:36:18] WARNING: no name column found on line 24 -223: [07:36:18] WARNING: no name column found on line 25 -223: [07:36:18] WARNING: no name column found on line 26 -223: [07:36:18] WARNING: no name column found on line 27 -223: [07:36:18] WARNING: no name column found on line 28 -223: [07:36:18] WARNING: no name column found on line 29 -223: [07:36:18] WARNING: no name column found on line 30 -223: [07:36:18] WARNING: no name column found on line 31 -223: [07:36:18] WARNING: no name column found on line 32 -223: [07:36:18] WARNING: no name column found on line 33 -223: [07:36:18] WARNING: no name column found on line 34 -223: [07:36:18] WARNING: no name column found on line 35 -223: [07:36:18] WARNING: no name column found on line 36 -223: [07:36:18] WARNING: no name column found on line 37 -223: [07:36:18] WARNING: no name column found on line 38 -223: [07:36:18] WARNING: no name column found on line 39 -223: [07:36:18] WARNING: no name column found on line 40 -223: [07:36:18] WARNING: no name column found on line 41 -223: [07:36:18] WARNING: no name column found on line 42 -223: [07:36:18] WARNING: no name column found on line 43 -223: [07:36:18] WARNING: no name column found on line 44 -223: [07:36:18] WARNING: no name column found on line 45 -223: [07:36:18] WARNING: no name column found on line 46 -223: [07:36:18] WARNING: no name column found on line 47 -223: [07:36:18] WARNING: no name column found on line 48 -223: [07:36:18] WARNING: no name column found on line 49 -223: [07:36:18] WARNING: no name column found on line 50 -223: [07:36:18] WARNING: no name column found on line 51 -223: [07:36:18] WARNING: no name column found on line 52 -223: [07:36:18] WARNING: no name column found on line 53 -223: [07:36:18] WARNING: no name column found on line 54 -223: [07:36:18] WARNING: no name column found on line 55 -223: [07:36:18] WARNING: no name column found on line 56 -223: [07:36:18] WARNING: no name column found on line 57 -223: [07:36:18] WARNING: no name column found on line 58 -223: [07:36:18] WARNING: no name column found on line 59 -223: [07:36:18] WARNING: no name column found on line 60 -223: [07:36:18] WARNING: no name column found on line 61 -223: [07:36:18] WARNING: no name column found on line 62 -223: [07:36:18] WARNING: no name column found on line 63 -223: [07:36:18] WARNING: no name column found on line 64 -223: [07:36:18] WARNING: no name column found on line 65 -223: [07:36:18] WARNING: no name column found on line 66 -223: [07:36:18] WARNING: no name column found on line 67 -223: [07:36:18] WARNING: no name column found on line 68 -223: [07:36:18] WARNING: no name column found on line 69 -223: [07:36:18] WARNING: no name column found on line 70 -223: [07:36:18] WARNING: no name column found on line 71 -223: [07:36:18] WARNING: no name column found on line 72 -223: [07:36:18] WARNING: no name column found on line 73 -223: [07:36:18] WARNING: no name column found on line 74 -223: [07:36:18] WARNING: no name column found on line 75 -223: [07:36:18] WARNING: no name column found on line 76 -223: [07:36:18] WARNING: no name column found on line 77 -223: [07:36:18] WARNING: no name column found on line 78 -223: [07:36:18] WARNING: no name column found on line 79 -223: [07:36:18] WARNING: no name column found on line 80 -223: [07:36:18] WARNING: no name column found on line 81 -223: [07:36:18] WARNING: no name column found on line 82 -223: [07:36:18] WARNING: no name column found on line 83 -223: [07:36:18] WARNING: no name column found on line 84 -223: [07:36:18] WARNING: no name column found on line 85 -223: [07:36:18] WARNING: no name column found on line 86 -223: [07:36:18] WARNING: no name column found on line 87 -223: [07:36:18] WARNING: no name column found on line 88 -223: [07:36:18] WARNING: no name column found on line 89 -223: [07:36:18] WARNING: no name column found on line 90 -223: [07:36:18] WARNING: no name column found on line 91 -223: [07:36:18] WARNING: no name column found on line 92 -223: [07:36:18] WARNING: no name column found on line 93 -223: [07:36:18] WARNING: no name column found on line 94 -223: [07:36:18] WARNING: no name column found on line 95 -223: [07:36:18] WARNING: no name column found on line 96 -223: [07:36:18] WARNING: no name column found on line 97 -223: [07:36:18] WARNING: no name column found on line 98 -223: [07:36:18] WARNING: no name column found on line 99 -223: [07:36:18] WARNING: no name column found on line 100 -223: [07:36:18] WARNING: no name column found on line 101 -223: [07:36:18] WARNING: no name column found on line 102 -223: [07:36:18] WARNING: no name column found on line 103 -223: [07:36:18] WARNING: no name column found on line 104 -223: [07:36:18] WARNING: no name column found on line 105 -223: [07:36:18] WARNING: no name column found on line 106 -223: [07:36:18] WARNING: no name column found on line 107 -223: [07:36:18] WARNING: no name column found on line 108 -223: [07:36:18] WARNING: no name column found on line 109 -223: [07:36:18] WARNING: no name column found on line 110 -223: [07:36:18] WARNING: no name column found on line 111 -223: [07:36:18] WARNING: no name column found on line 112 -223: [07:36:18] WARNING: no name column found on line 113 -223: [07:36:18] WARNING: no name column found on line 114 -223: [07:36:18] WARNING: no name column found on line 115 -223: [07:36:18] WARNING: no name column found on line 116 -223: [07:36:18] WARNING: no name column found on line 117 -223: [07:36:18] WARNING: no name column found on line 118 -223: [07:36:18] WARNING: no name column found on line 119 -223: [07:36:18] WARNING: no name column found on line 120 -223: [07:36:18] WARNING: no name column found on line 121 -223: [07:36:18] WARNING: no name column found on line 122 -223: [07:36:18] WARNING: no name column found on line 123 -223: [07:36:18] WARNING: no name column found on line 124 -223: [07:36:18] WARNING: no name column found on line 125 -223: [07:36:18] WARNING: no name column found on line 126 -223: [07:36:18] WARNING: no name column found on line 127 -223: [07:36:18] WARNING: no name column found on line 128 -223: [07:36:18] WARNING: no name column found on line 129 -223: [07:36:18] WARNING: no name column found on line 130 -223: [07:36:18] WARNING: no name column found on line 131 -223: [07:36:18] WARNING: no name column found on line 132 -223: [07:36:18] WARNING: no name column found on line 133 -223: [07:36:18] WARNING: no name column found on line 134 -223: [07:36:18] WARNING: no name column found on line 135 -223: [07:36:18] WARNING: no name column found on line 136 -223: [07:36:18] WARNING: no name column found on line 137 -223: [07:36:18] WARNING: no name column found on line 138 -223: [07:36:18] WARNING: no name column found on line 139 -223: [07:36:18] WARNING: no name column found on line 140 -223: [07:36:18] WARNING: no name column found on line 141 -223: [07:36:18] WARNING: no name column found on line 142 -223: [07:36:18] WARNING: no name column found on line 143 -223: [07:36:18] WARNING: no name column found on line 144 -223: [07:36:18] WARNING: no name column found on line 145 -223: [07:36:18] WARNING: no name column found on line 146 -223: [07:36:18] WARNING: no name column found on line 147 -223: [07:36:18] WARNING: no name column found on line 148 -223: [07:36:18] WARNING: no name column found on line 149 -223: [07:36:18] WARNING: no name column found on line 150 -223: [07:36:18] WARNING: no name column found on line 151 -223: [07:36:18] WARNING: no name column found on line 152 -223: [07:36:18] WARNING: no name column found on line 153 -223: [07:36:18] WARNING: no name column found on line 154 -223: [07:36:18] WARNING: no name column found on line 155 -223: [07:36:18] WARNING: no name column found on line 156 -223: [07:36:18] WARNING: no name column found on line 157 -223: [07:36:18] WARNING: no name column found on line 158 -223: [07:36:18] WARNING: no name column found on line 159 -223: [07:36:18] WARNING: no name column found on line 160 -223: [07:36:18] WARNING: no name column found on line 161 -223: [07:36:18] WARNING: no name column found on line 162 -223: [07:36:18] WARNING: no name column found on line 163 -223: [07:36:18] WARNING: no name column found on line 164 -223: [07:36:18] WARNING: no name column found on line 165 -223: [07:36:18] WARNING: no name column found on line 166 -223: [07:36:18] WARNING: no name column found on line 167 -223: [07:36:18] WARNING: no name column found on line 168 -223: [07:36:18] WARNING: no name column found on line 169 -223: [07:36:18] WARNING: no name column found on line 170 -223: [07:36:18] WARNING: no name column found on line 171 -223: [07:36:18] WARNING: no name column found on line 172 -223: [07:36:18] WARNING: no name column found on line 173 -223: [07:36:18] WARNING: no name column found on line 174 -223: [07:36:18] WARNING: no name column found on line 175 -223: [07:36:18] WARNING: no name column found on line 176 -223: [07:36:18] WARNING: no name column found on line 177 -223: [07:36:18] WARNING: no name column found on line 178 -223: [07:36:18] WARNING: no name column found on line 179 -223: [07:36:18] WARNING: no name column found on line 180 -223: [07:36:18] WARNING: no name column found on line 181 -223: [07:36:18] WARNING: no name column found on line 182 -223: [07:36:18] WARNING: no name column found on line 183 -223: [07:36:18] WARNING: no name column found on line 184 -223: [07:36:18] WARNING: no name column found on line 185 -223: [07:36:18] WARNING: no name column found on line 186 -223: [07:36:18] WARNING: no name column found on line 187 -223: [07:36:18] WARNING: no name column found on line 188 -223: [07:36:18] WARNING: no name column found on line 189 -223: [07:36:18] WARNING: no name column found on line 190 -223: [07:36:18] WARNING: no name column found on line 191 -223: [07:36:18] WARNING: no name column found on line 192 -223: [07:36:18] WARNING: no name column found on line 193 -223: [07:36:18] WARNING: no name column found on line 194 -223: [07:36:18] WARNING: no name column found on line 195 -223: [07:36:18] WARNING: no name column found on line 196 -223: [07:36:18] WARNING: no name column found on line 197 -223: [07:36:18] WARNING: no name column found on line 198 -223: [07:36:18] WARNING: no name column found on line 199 -223: [07:36:18] WARNING: no name column found on line 200 -223: [07:36:18] WARNING: no name column found on line 201 -223: [07:36:18] WARNING: no name column found on line 202 -223: [07:36:18] WARNING: no name column found on line 203 -223: [07:36:18] WARNING: no name column found on line 204 -223: [07:36:18] WARNING: no name column found on line 205 -223: [07:36:18] WARNING: no name column found on line 206 -223: [07:36:18] WARNING: no name column found on line 207 -223: [07:36:18] WARNING: no name column found on line 208 -223: [07:36:18] WARNING: no name column found on line 209 -223: [07:36:18] WARNING: no name column found on line 210 -223: [07:36:18] WARNING: no name column found on line 211 -223: [07:36:18] WARNING: no name column found on line 212 -223: [07:36:18] WARNING: no name column found on line 213 -223: [07:36:18] WARNING: no name column found on line 214 -223: [07:36:18] WARNING: no name column found on line 215 -223: [07:36:18] WARNING: no name column found on line 216 +133: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 +133: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] +133: [04:08:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +133: [04:08:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +223: ..[04:09:02] WARNING: not removing hydrogen atom without neighbors +223: .[04:09:02] WARNING: not removing hydrogen atom without neighbors +223: .[04:09:02] WARNING: no name column found on line 1 +223: [04:09:02] WARNING: no name column found on line 2 +223: [04:09:02] WARNING: no name column found on line 3 +223: [04:09:02] WARNING: no name column found on line 4 +223: [04:09:02] WARNING: no name column found on line 5 +223: [04:09:02] WARNING: no name column found on line 6 +223: [04:09:02] WARNING: no name column found on line 7 +223: [04:09:02] WARNING: no name column found on line 8 +223: [04:09:02] WARNING: no name column found on line 9 +223: [04:09:02] WARNING: no name column found on line 10 +223: [04:09:02] WARNING: no name column found on line 11 +223: [04:09:02] WARNING: no name column found on line 12 +223: [04:09:02] WARNING: no name column found on line 13 +223: [04:09:02] WARNING: no name column found on line 14 +223: [04:09:02] WARNING: no name column found on line 15 +223: [04:09:02] WARNING: no name column found on line 16 +223: [04:09:02] WARNING: no name column found on line 17 +223: [04:09:02] WARNING: no name column found on line 18 +223: [04:09:02] WARNING: no name column found on line 19 +223: [04:09:02] WARNING: no name column found on line 20 +223: [04:09:02] WARNING: no name column found on line 21 +223: [04:09:02] WARNING: no name column found on line 22 +223: [04:09:02] WARNING: no name column found on line 23 +223: [04:09:02] WARNING: no name column found on line 24 +223: [04:09:02] WARNING: no name column found on line 25 +223: [04:09:02] WARNING: no name column found on line 26 +223: [04:09:02] WARNING: no name column found on line 27 +223: [04:09:02] WARNING: no name column found on line 28 +223: [04:09:02] WARNING: no name column found on line 29 +223: [04:09:02] WARNING: no name column found on line 30 +223: [04:09:02] WARNING: no name column found on line 31 +223: [04:09:02] WARNING: no name column found on line 32 +223: [04:09:02] WARNING: no name column found on line 33 +223: [04:09:02] WARNING: no name column found on line 34 +223: [04:09:02] WARNING: no name column found on line 35 +223: [04:09:02] WARNING: no name column found on line 36 +223: [04:09:02] WARNING: no name column found on line 37 +223: [04:09:02] WARNING: no name column found on line 38 +223: [04:09:02] WARNING: no name column found on line 39 +223: [04:09:02] WARNING: no name column found on line 40 +223: [04:09:02] WARNING: no name column found on line 41 +223: [04:09:02] WARNING: no name column found on line 42 +223: [04:09:02] WARNING: no name column found on line 43 +223: [04:09:02] WARNING: no name column found on line 44 +223: [04:09:02] WARNING: no name column found on line 45 +223: [04:09:02] WARNING: no name column found on line 46 +223: [04:09:02] WARNING: no name column found on line 47 +223: [04:09:02] WARNING: no name column found on line 48 +223: [04:09:02] WARNING: no name column found on line 49 +223: [04:09:02] WARNING: no name column found on line 50 +223: [04:09:02] WARNING: no name column found on line 51 +223: [04:09:02] WARNING: no name column found on line 52 +223: [04:09:02] WARNING: no name column found on line 53 +223: [04:09:02] WARNING: no name column found on line 54 +223: [04:09:02] WARNING: no name column found on line 55 +223: [04:09:02] WARNING: no name column found on line 56 +223: [04:09:02] WARNING: no name column found on line 57 +223: [04:09:02] WARNING: no name column found on line 58 +223: [04:09:02] WARNING: no name column found on line 59 +223: [04:09:02] WARNING: no name column found on line 60 +223: [04:09:02] WARNING: no name column found on line 61 +223: [04:09:02] WARNING: no name column found on line 62 +223: [04:09:02] WARNING: no name column found on line 63 +223: [04:09:02] WARNING: no name column found on line 64 +223: [04:09:02] WARNING: no name column found on line 65 +223: [04:09:02] WARNING: no name column found on line 66 +223: [04:09:02] WARNING: no name column found on line 67 +223: [04:09:02] WARNING: no name column found on line 68 +223: [04:09:02] WARNING: no name column found on line 69 +223: [04:09:02] WARNING: no name column found on line 70 +223: [04:09:02] WARNING: no name column found on line 71 +223: [04:09:02] WARNING: no name column found on line 72 +223: [04:09:02] WARNING: no name column found on line 73 +223: [04:09:02] WARNING: no name column found on line 74 +223: [04:09:02] WARNING: no name column found on line 75 +223: [04:09:02] WARNING: no name column found on line 76 +223: [04:09:02] WARNING: no name column found on line 77 +223: [04:09:02] WARNING: no name column found on line 78 +223: [04:09:02] WARNING: no name column found on line 79 +223: [04:09:02] WARNING: no name column found on line 80 +223: [04:09:02] WARNING: no name column found on line 81 +223: [04:09:02] WARNING: no name column found on line 82 +223: [04:09:02] WARNING: no name column found on line 83 +223: [04:09:02] WARNING: no name column found on line 84 +223: [04:09:02] WARNING: no name column found on line 85 +223: [04:09:02] WARNING: no name column found on line 86 +223: [04:09:02] WARNING: no name column found on line 87 +223: [04:09:02] WARNING: no name column found on line 88 +223: [04:09:02] WARNING: no name column found on line 89 +223: [04:09:02] WARNING: no name column found on line 90 +223: [04:09:02] WARNING: no name column found on line 91 +223: [04:09:02] WARNING: no name column found on line 92 +223: [04:09:02] WARNING: no name column found on line 93 +223: [04:09:02] WARNING: no name column found on line 94 +223: [04:09:02] WARNING: no name column found on line 95 +223: [04:09:02] WARNING: no name column found on line 96 +223: [04:09:02] WARNING: no name column found on line 97 +223: [04:09:02] WARNING: no name column found on line 98 +223: [04:09:02] WARNING: no name column found on line 99 +223: [04:09:02] WARNING: no name column found on line 100 +223: [04:09:02] WARNING: no name column found on line 101 +223: [04:09:02] WARNING: no name column found on line 102 +223: [04:09:02] WARNING: no name column found on line 103 +223: [04:09:02] WARNING: no name column found on line 104 +223: [04:09:02] WARNING: no name column found on line 105 +223: [04:09:02] WARNING: no name column found on line 106 +223: [04:09:02] WARNING: no name column found on line 107 +223: [04:09:02] WARNING: no name column found on line 108 +223: [04:09:02] WARNING: no name column found on line 109 +223: [04:09:02] WARNING: no name column found on line 110 +223: [04:09:02] WARNING: no name column found on line 111 +223: [04:09:02] WARNING: no name column found on line 112 +223: [04:09:02] WARNING: no name column found on line 113 +223: [04:09:02] WARNING: no name column found on line 114 +223: [04:09:02] WARNING: no name column found on line 115 +223: [04:09:02] WARNING: no name column found on line 116 +223: [04:09:02] WARNING: no name column found on line 117 +223: [04:09:02] WARNING: no name column found on line 118 +223: [04:09:02] WARNING: no name column found on line 119 +223: [04:09:02] WARNING: no name column found on line 120 +223: [04:09:02] WARNING: no name column found on line 121 +223: [04:09:02] WARNING: no name column found on line 122 +223: [04:09:02] WARNING: no name column found on line 123 +223: [04:09:02] WARNING: no name column found on line 124 +223: [04:09:02] WARNING: no name column found on line 125 +223: [04:09:02] WARNING: no name column found on line 126 +223: [04:09:02] WARNING: no name column found on line 127 +223: [04:09:02] WARNING: no name column found on line 128 +223: [04:09:02] WARNING: no name column found on line 129 +223: [04:09:02] WARNING: no name column found on line 130 +223: [04:09:02] WARNING: no name column found on line 131 +223: [04:09:02] WARNING: no name column found on line 132 +223: [04:09:02] WARNING: no name column found on line 133 +223: [04:09:02] WARNING: no name column found on line 134 +223: [04:09:02] WARNING: no name column found on line 135 +223: [04:09:02] WARNING: no name column found on line 136 +223: [04:09:02] WARNING: no name column found on line 137 +223: [04:09:02] WARNING: no name column found on line 138 +223: [04:09:02] WARNING: no name column found on line 139 +223: [04:09:02] WARNING: no name column found on line 140 +223: [04:09:02] WARNING: no name column found on line 141 +223: [04:09:02] WARNING: no name column found on line 142 +223: [04:09:02] WARNING: no name column found on line 143 +223: [04:09:02] WARNING: no name column found on line 144 +223: [04:09:02] WARNING: no name column found on line 145 +223: [04:09:02] WARNING: no name column found on line 146 +223: [04:09:02] WARNING: no name column found on line 147 +223: [04:09:02] WARNING: no name column found on line 148 +223: [04:09:02] WARNING: no name column found on line 149 +223: [04:09:02] WARNING: no name column found on line 150 +223: [04:09:02] WARNING: no name column found on line 151 +223: [04:09:02] WARNING: no name column found on line 152 +223: [04:09:02] WARNING: no name column found on line 153 +223: [04:09:02] WARNING: no name column found on line 154 +223: [04:09:02] WARNING: no name column found on line 155 +223: [04:09:02] WARNING: no name column found on line 156 +223: [04:09:02] WARNING: no name column found on line 157 +223: [04:09:02] WARNING: no name column found on line 158 +223: [04:09:02] WARNING: no name column found on line 159 +223: [04:09:02] WARNING: no name column found on line 160 +223: [04:09:02] WARNING: no name column found on line 161 +223: [04:09:02] WARNING: no name column found on line 162 +223: [04:09:02] WARNING: no name column found on line 163 +223: [04:09:02] WARNING: no name column found on line 164 +223: [04:09:02] WARNING: no name column found on line 165 +223: [04:09:02] WARNING: no name column found on line 166 +223: [04:09:02] WARNING: no name column found on line 167 +223: [04:09:02] WARNING: no name column found on line 168 +223: [04:09:02] WARNING: no name column found on line 169 +223: [04:09:02] WARNING: no name column found on line 170 +223: [04:09:02] WARNING: no name column found on line 171 +223: [04:09:02] WARNING: no name column found on line 172 +223: [04:09:02] WARNING: no name column found on line 173 +223: [04:09:02] WARNING: no name column found on line 174 +223: [04:09:02] WARNING: no name column found on line 175 +223: [04:09:02] WARNING: no name column found on line 176 +223: [04:09:02] WARNING: no name column found on line 177 +223: [04:09:02] WARNING: no name column found on line 178 +223: [04:09:02] WARNING: no name column found on line 179 +223: [04:09:02] WARNING: no name column found on line 180 +223: [04:09:02] WARNING: no name column found on line 181 +223: [04:09:02] WARNING: no name column found on line 182 +223: [04:09:02] WARNING: no name column found on line 183 +223: [04:09:02] WARNING: no name column found on line 184 +223: [04:09:02] WARNING: no name column found on line 185 +223: [04:09:02] WARNING: no name column found on line 186 +223: [04:09:02] WARNING: no name column found on line 187 +223: [04:09:02] WARNING: no name column found on line 188 +223: [04:09:02] WARNING: no name column found on line 189 +223: [04:09:02] WARNING: no name column found on line 190 +223: [04:09:02] WARNING: no name column found on line 191 +223: [04:09:02] WARNING: no name column found on line 192 +223: [04:09:02] WARNING: no name column found on line 193 +223: [04:09:02] WARNING: no name column found on line 194 +223: [04:09:02] WARNING: no name column found on line 195 +223: [04:09:02] WARNING: no name column found on line 196 +223: [04:09:02] WARNING: no name column found on line 197 +223: [04:09:02] WARNING: no name column found on line 198 +223: [04:09:02] WARNING: no name column found on line 199 +223: [04:09:02] WARNING: no name column found on line 200 +223: [04:09:02] WARNING: no name column found on line 201 +223: [04:09:02] WARNING: no name column found on line 202 +223: [04:09:02] WARNING: no name column found on line 203 +223: [04:09:02] WARNING: no name column found on line 204 +223: [04:09:02] WARNING: no name column found on line 205 +223: [04:09:02] WARNING: no name column found on line 206 +223: [04:09:02] WARNING: no name column found on line 207 +223: [04:09:02] WARNING: no name column found on line 208 +223: [04:09:02] WARNING: no name column found on line 209 +223: [04:09:02] WARNING: no name column found on line 210 +223: [04:09:02] WARNING: no name column found on line 211 +223: [04:09:02] WARNING: no name column found on line 212 +223: [04:09:02] WARNING: no name column found on line 213 +223: [04:09:02] WARNING: no name column found on line 214 +223: [04:09:02] WARNING: no name column found on line 215 +223: [04:09:02] WARNING: no name column found on line 216 223: ...... 223: ---------------------------------------------------------------------- -223: Ran 10 tests in 0.162s +223: Ran 10 tests in 0.197s 223: 223: OK -133: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 -133: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] +133: [04:09:08] Molecule does not have explicit Hs. Consider calling AddHs() +221/223 Test #133: testDistGeomHelpers .................... Passed 314.91 sec 223: .................. 223: ---------------------------------------------------------------------- -223: Ran 18 tests in 0.901s +223: Ran 18 tests in 2.259s 223: 223: OK -133: [07:36:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -133: [07:36:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 223: ... 223: ---------------------------------------------------------------------- -223: Ran 3 tests in 0.068s +223: Ran 3 tests in 0.178s 223: 223: OK 223: ........ 223: ---------------------------------------------------------------------- -223: Ran 8 tests in 0.029s +223: Ran 8 tests in 0.105s 223: 223: OK 223: .. 223: ---------------------------------------------------------------------- -223: Ran 2 tests in 0.015s +223: Ran 2 tests in 0.052s 223: 223: OK 223: .. 223: ---------------------------------------------------------------------- -223: Ran 2 tests in 0.017s +223: Ran 2 tests in 0.041s 223: 223: OK 223: . 223: ---------------------------------------------------------------------- -223: Ran 1 test in 0.088s +223: Ran 1 test in 0.100s 223: 223: OK 223: ........ 223: ---------------------------------------------------------------------- -223: Ran 8 tests in 0.002s +223: Ran 8 tests in 0.003s 223: 223: OK 223: ... 223: ---------------------------------------------------------------------- -223: Ran 3 tests in 0.006s +223: Ran 3 tests in 0.008s 223: 223: OK 223: ... @@ -28178,29 +28211,27 @@ 223: OK 223: .... 223: ---------------------------------------------------------------------- -223: Ran 4 tests in 0.005s +223: Ran 4 tests in 0.006s 223: 223: OK 223: ....... 223: ---------------------------------------------------------------------- -223: Ran 7 tests in 0.014s +223: Ran 7 tests in 0.030s 223: 223: OK 223: .... 223: ---------------------------------------------------------------------- -223: Ran 4 tests in 0.021s +223: Ran 4 tests in 0.077s 223: 223: OK -133: [07:36:29] Molecule does not have explicit Hs. Consider calling AddHs() -222/223 Test #133: testDistGeomHelpers .................... Passed 90.96 sec 223: .... 223: ---------------------------------------------------------------------- -223: Ran 4 tests in 3.014s +223: Ran 4 tests in 6.949s 223: 223: OK 223: .......... 223: ---------------------------------------------------------------------- -223: Ran 10 tests in 0.052s +223: Ran 10 tests in 0.151s 223: 223: OK 223: . @@ -28210,29 +28241,29 @@ 223: OK 223: .......... 223: ---------------------------------------------------------------------- -223: Ran 10 tests in 0.006s +223: Ran 10 tests in 0.016s 223: 223: OK 223: ..... 223: ---------------------------------------------------------------------- -223: Ran 5 tests in 0.078s +223: Ran 5 tests in 0.120s 223: 223: OK -223: .........[07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -223: [07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -223: [07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -223: [07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -223: .......[07:36:36] Molecule does not have explicit Hs. Consider calling AddHs() -223: [07:36:36] Molecule does not have explicit Hs. Consider calling AddHs() +223: .........[04:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +223: [04:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +223: [04:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +223: [04:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +223: .......[04:09:46] Molecule does not have explicit Hs. Consider calling AddHs() +223: [04:09:46] Molecule does not have explicit Hs. Consider calling AddHs() 223: ..... 223: ---------------------------------------------------------------------- -223: Ran 21 tests in 5.392s +223: Ran 21 tests in 10.379s 223: 223: OK 223: mol_197 223: 219.10,35.89,110.98,11.56,110.32,11.04,95.23,10.25,0.00 223: mol_223 -223: 243.67,7.40,134.64,0.81,134.56,0.81,85.50,0.37,0.00 +223: 243.69,7.30,134.82,1.04,134.75,1.04,85.57,0.33,0.00 223: mol_269 223: 216.26,5.67,105.00,0.87,103.81,0.89,89.27,0.92,6.00 223: . @@ -28240,7 +28271,7 @@ 223: Ran 1 test in 0.000s 223: 223: OK -223: ...[07:36:37] +223: ...[04:09:48] 223: 223: **** 223: Pre-condition Violation @@ -28251,63 +28282,63 @@ 223: 223: . 223: ---------------------------------------------------------------------- -223: Ran 4 tests in 0.013s +223: Ran 4 tests in 0.029s 223: 223: OK 223: .. 223: ---------------------------------------------------------------------- -223: Ran 2 tests in 6.519s +223: Ran 2 tests in 21.410s 223: 223: OK 223: .. 223: ---------------------------------------------------------------------- -223: Ran 2 tests in 0.111s +223: Ran 2 tests in 0.416s 223: 223: OK 223: ... 223: ---------------------------------------------------------------------- -223: Ran 3 tests in 0.014s +223: Ran 3 tests in 0.030s 223: 223: OK 223: .... 223: ---------------------------------------------------------------------- -223: Ran 4 tests in 0.021s +223: Ran 4 tests in 0.031s 223: 223: OK -223: .....[07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors -223: [07:36:46] WARNING: not removing hydrogen atom without neighbors +223: .....[04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors +223: [04:10:17] WARNING: not removing hydrogen atom without neighbors 223: ..... 223: ---------------------------------------------------------------------- -223: Ran 10 tests in 0.350s +223: Ran 10 tests in 0.941s 223: 223: OK 223: ssssss..........s/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit/Chem/Draw/__init__.py:237: DeprecationWarning: legacy DrawingOptions not translated for new drawing code, please update manually 223: warnings.warn( 223: ..... 223: ---------------------------------------------------------------------- -223: Ran 22 tests in 4.573s +223: Ran 22 tests in 13.409s 223: 223: OK (skipped=7) 223: sss. 223: ---------------------------------------------------------------------- -223: Ran 4 tests in 0.522s +223: Ran 4 tests in 0.748s 223: 223: OK (skipped=3) 223: ssss @@ -28317,50 +28348,50 @@ 223: OK (skipped=4) 223: .......... 223: ---------------------------------------------------------------------- -223: Ran 10 tests in 0.827s +223: Ran 10 tests in 1.107s 223: 223: OK -223: ...[07:36:55] SMARTS Parse Error: syntax error while parsing: boromicacid -223: [07:36:55] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -223: [07:36:55] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -223: [07:36:55] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -223: [07:36:55] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -223: [07:36:55] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -223: [07:36:55] reaction has no reactants -223: [07:36:55] reaction has no products -223: [07:36:55] initialization failed -223: [07:36:55] reaction has no reactants -223: [07:36:55] reaction has no products +223: ...[04:10:41] SMARTS Parse Error: syntax error while parsing: boromicacid +223: [04:10:41] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +223: [04:10:41] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +223: [04:10:41] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +223: [04:10:41] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +223: [04:10:41] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +223: [04:10:41] reaction has no reactants +223: [04:10:41] reaction has no products +223: [04:10:41] initialization failed +223: [04:10:41] reaction has no reactants +223: [04:10:41] reaction has no products 223: . 223: ---------------------------------------------------------------------- -223: Ran 4 tests in 0.026s +223: Ran 4 tests in 0.049s 223: 223: OK 223: ['C[C@@H](F)CN', 'C[C@@H](F)CN |a:1|', 'C[C@H](F)CN |o1:1|', 'C[C@H](F)CN |&1:1|'] 223: .... 223: ---------------------------------------------------------------------- -223: Ran 4 tests in 0.011s +223: Ran 4 tests in 0.018s 223: 223: OK 223: ........................ 223: ---------------------------------------------------------------------- -223: Ran 24 tests in 0.095s +223: Ran 24 tests in 0.168s 223: 223: OK 223: !!! TEST FAILURE: python UnitTestInchi.py {} 223: !!! TEST FAILURE: python UnitTestPandasTools.py {} -223/223 Test #223: pythonTestDirChem ......................***Failed 114.27 sec +222/223 Test #223: pythonTestDirChem ......................***Failed 358.49 sec ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.167s +Ran 7 tests in 0.522s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.047s +Ran 6 tests in 0.116s OK -....[07:35:04] +....[04:04:51] **** Pre-condition Violation @@ -28371,103 +28402,103 @@ . ---------------------------------------------------------------------- -Ran 5 tests in 0.031s +Ran 5 tests in 0.030s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.024s +Ran 4 tests in 0.051s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.012s +Ran 2 tests in 0.036s OK ...................... ---------------------------------------------------------------------- -Ran 22 tests in 0.039s +Ran 22 tests in 0.113s OK .....s.................ss ---------------------------------------------------------------------- -Ran 25 tests in 0.115s +Ran 25 tests in 0.457s OK (skipped=3) ..s ---------------------------------------------------------------------- -Ran 3 tests in 0.143s +Ran 3 tests in 0.285s OK (skipped=1) ................................... ---------------------------------------------------------------------- -Ran 35 tests in 1.062s +Ran 35 tests in 1.135s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.012s +Ran 4 tests in 0.048s OK . ---------------------------------------------------------------------- -Ran 1 test in 0.009s +Ran 1 test in 0.052s OK ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.029s +Ran 7 tests in 0.159s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.031s +Ran 3 tests in 0.212s OK .ss.ss....... ---------------------------------------------------------------------- -Ran 13 tests in 1.010s +Ran 13 tests in 2.145s OK (skipped=4) -[07:35:10] Molecule does not have explicit Hs. Consider calling AddHs() -.[07:35:10] Molecule does not have explicit Hs. Consider calling AddHs() -....................[07:35:37] WARNING: More than one matching pattern found - picking one +[04:05:09] Molecule does not have explicit Hs. Consider calling AddHs() +.[04:05:09] Molecule does not have explicit Hs. Consider calling AddHs() +....................[04:07:01] WARNING: More than one matching pattern found - picking one -[07:35:37] WARNING: More than one matching pattern found - picking one +[04:07:01] WARNING: More than one matching pattern found - picking one -.[07:35:37] WARNING: More than one matching pattern found - picking one +.[04:07:01] WARNING: More than one matching pattern found - picking one ... ---------------------------------------------------------------------- -Ran 25 tests in 30.624s +Ran 25 tests in 125.061s OK -{'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl'} -{'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl'} -{'F[C@H](Cl)[C@@H](F)Cl', 'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@H](F)Cl'} +{'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl'} +{'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl'} +{'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@H](F)Cl'} !!!! ['C[C@H]([C@H](C)Br)[C@@H](C)F', 'C[C@@H]([C@@H](C)F)[C@@H](C)Br', 'C[C@@H]([C@H](C)Br)[C@@H](C)F', 'C[C@H]([C@@H](C)F)[C@@H](C)Br', 'C[C@@H]([C@H](C)F)[C@H](C)Br', 'C[C@@H]([C@H](C)F)[C@@H](C)Br', 'C[C@H]([C@H](C)F)[C@H](C)Br', 'C[C@H]([C@H](C)F)[C@@H](C)Br'] ........ ---------------------------------------------------------------------- -Ran 8 tests in 0.136s +Ran 8 tests in 0.168s OK -.[07:35:42] Molecule does not have explicit Hs. Consider calling AddHs() -.....[07:35:46] WARNING: not removing hydrogen atom without neighbors -[07:35:46] WARNING: not removing hydrogen atom without neighbors -[07:35:46] WARNING: not removing hydrogen atom without neighbors -....[07:35:46] WARNING: not removing hydrogen atom without neighbors +.[04:07:16] Molecule does not have explicit Hs. Consider calling AddHs() +.....[04:07:25] WARNING: not removing hydrogen atom without neighbors +[04:07:25] WARNING: not removing hydrogen atom without neighbors +[04:07:25] WARNING: not removing hydrogen atom without neighbors +....[04:07:25] WARNING: not removing hydrogen atom without neighbors ...... ---------------------------------------------------------------------- -Ran 16 tests in 3.589s +Ran 16 tests in 8.580s OK -[07:35:46] WARNING: Omitted undefined stereo +[04:07:26] WARNING: Omitted undefined stereo -[07:35:46] WARNING: Proton(s) added/removed +[04:07:26] WARNING: Proton(s) added/removed -..[07:35:48] ERROR: Add/Remove protons error; *Conversion failed* +..[04:07:29] ERROR: Add/Remove protons error; *Conversion failed* -[07:35:48] ERROR: Add/Remove protons error; *Conversion failed* +[04:07:29] ERROR: Add/Remove protons error; *Conversion failed* E.... ====================================================================== @@ -28480,19 +28511,19 @@ AttributeError: 'NoneType' object has no attribute 'GetAtoms' ---------------------------------------------------------------------- -Ran 7 tests in 2.440s +Ran 7 tests in 3.547s FAILED (errors=1) InChI write Summary: 1160 identical, 0 suffix variance, 21 reasonable .... ---------------------------------------------------------------------- -Ran 4 tests in 1.448s +Ran 4 tests in 4.878s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.347s +Ran 6 tests in 0.647s OK /build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestPandasTools.py:218: SyntaxWarning: invalid escape sequence '\O' @@ -28545,7 +28576,7 @@ Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestPandasTools.py", line 229, in testPandasShouldShowMoleculesWhenTruncating self.assertIn('data-content="rdkit/molecule"', html_output) -AssertionError: 'data-content="rdkit/molecule"' not found in '
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
Molecule ChEMBL IDMolecule NameMolecule Max PhaseMolecular Weight#RO5 Violations...Source DescriptionDocument JournalDocument YearCell ChEMBL IDROMol
0"CHEMBL543779"NaN0341.860...Scientific LiteratureJ. Med. Chem.1986NaN<rdkit.Chem.rdchem.Mol object at 0x7f875127b060>
\n
' +AssertionError: 'data-content="rdkit/molecule"' not found in '
\n\n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
Molecule ChEMBL IDMolecule NameMolecule Max PhaseMolecular Weight#RO5 Violations...Source DescriptionDocument JournalDocument YearCell ChEMBL IDROMol
0"CHEMBL543779"NaN0341.860...Scientific LiteratureJ. Med. Chem.1986NaN<rdkit.Chem.rdchem.Mol object at 0x7f963fbd6f80>
\n
' ====================================================================== FAIL: test_RestoreMonkeyPatch (__main__.TestPandasTools.test_RestoreMonkeyPatch) @@ -28553,306 +28584,306 @@ Traceback (most recent call last): File "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/UnitTestPandasTools.py", line 64, in test_RestoreMonkeyPatch self.assertIn('data:image/png;base64', html) -AssertionError: 'data:image/png;base64' not found in '\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
prop1prop2IDROMolprop3
012.34qweMethane<rdkit.Chem.rdchem.Mol object at 0x7f875127a180>NaN
1NaNrtzPeroxide<rdkit.Chem.rdchem.Mol object at 0x7f87508ba1f0>yxcv
' +AssertionError: 'data:image/png;base64' not found in '\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n
prop1prop2IDROMolprop3
012.34qweMethane<rdkit.Chem.rdchem.Mol object at 0x7f963fbd6420>NaN
1NaNrtzPeroxide<rdkit.Chem.rdchem.Mol object at 0x7f963f1fa180>yxcv
' ---------------------------------------------------------------------- -Ran 28 tests in 1.100s +Ran 28 tests in 5.075s FAILED (failures=2, skipped=2) -..............[07:36:03] WARNING: More than one matching pattern found - picking one +..............[04:08:16] WARNING: More than one matching pattern found - picking one -[07:36:03] WARNING: More than one matching pattern found - picking one +[04:08:16] WARNING: More than one matching pattern found - picking one -..[07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() -[07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() -[07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() -[07:36:03] Molecule does not have explicit Hs. Consider calling AddHs() +..[04:08:16] Molecule does not have explicit Hs. Consider calling AddHs() +[04:08:16] Molecule does not have explicit Hs. Consider calling AddHs() +[04:08:16] Molecule does not have explicit Hs. Consider calling AddHs() +[04:08:16] Molecule does not have explicit Hs. Consider calling AddHs() ......... ---------------------------------------------------------------------- -Ran 25 tests in 9.426s +Ran 25 tests in 26.695s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.054s +Ran 2 tests in 0.103s OK ..s... ---------------------------------------------------------------------- -Ran 6 tests in 1.017s +Ran 6 tests in 2.236s OK (skipped=1) .. ---------------------------------------------------------------------- -Ran 2 tests in 0.017s +Ran 2 tests in 0.070s OK .............. ---------------------------------------------------------------------- -Ran 14 tests in 2.605s +Ran 14 tests in 10.781s OK -..[07:36:18] WARNING: not removing hydrogen atom without neighbors -.[07:36:18] WARNING: not removing hydrogen atom without neighbors -.[07:36:18] WARNING: no name column found on line 1 -[07:36:18] WARNING: no name column found on line 2 -[07:36:18] WARNING: no name column found on line 3 -[07:36:18] WARNING: no name column found on line 4 -[07:36:18] WARNING: no name column found on line 5 -[07:36:18] WARNING: no name column found on line 6 -[07:36:18] WARNING: no name column found on line 7 -[07:36:18] WARNING: no name column found on line 8 -[07:36:18] WARNING: no name column found on line 9 -[07:36:18] WARNING: no name column found on line 10 -[07:36:18] WARNING: no name column found on line 11 -[07:36:18] WARNING: no name column found on line 12 -[07:36:18] WARNING: no name column found on line 13 -[07:36:18] WARNING: no name column found on line 14 -[07:36:18] WARNING: no name column found on line 15 -[07:36:18] WARNING: no name column found on line 16 -[07:36:18] WARNING: no name column found on line 17 -[07:36:18] WARNING: no name column found on line 18 -[07:36:18] WARNING: no name column found on line 19 -[07:36:18] WARNING: no name column found on line 20 -[07:36:18] WARNING: no name column found on line 21 -[07:36:18] WARNING: no name column found on line 22 -[07:36:18] WARNING: no name column found on line 23 -[07:36:18] WARNING: no name column found on line 24 -[07:36:18] WARNING: no name column found on line 25 -[07:36:18] WARNING: no name column found on line 26 -[07:36:18] WARNING: no name column found on line 27 -[07:36:18] WARNING: no name column found on line 28 -[07:36:18] WARNING: no name column found on line 29 -[07:36:18] WARNING: no name column found on line 30 -[07:36:18] WARNING: no name column found on line 31 -[07:36:18] WARNING: no name column found on line 32 -[07:36:18] WARNING: no name column found on line 33 -[07:36:18] WARNING: no name column found on line 34 -[07:36:18] WARNING: no name column found on line 35 -[07:36:18] WARNING: no name column found on line 36 -[07:36:18] WARNING: no name column found on line 37 -[07:36:18] WARNING: no name column found on line 38 -[07:36:18] WARNING: no name column found on line 39 -[07:36:18] WARNING: no name column found on line 40 -[07:36:18] WARNING: no name column found on line 41 -[07:36:18] WARNING: no name column found on line 42 -[07:36:18] WARNING: no name column found on line 43 -[07:36:18] WARNING: no name column found on line 44 -[07:36:18] WARNING: no name column found on line 45 -[07:36:18] WARNING: no name column found on line 46 -[07:36:18] WARNING: no name column found on line 47 -[07:36:18] WARNING: no name column found on line 48 -[07:36:18] WARNING: no name column found on line 49 -[07:36:18] WARNING: no name column found on line 50 -[07:36:18] WARNING: no name column found on line 51 -[07:36:18] WARNING: no name column found on line 52 -[07:36:18] WARNING: no name column found on line 53 -[07:36:18] WARNING: no name column found on line 54 -[07:36:18] WARNING: no name column found on line 55 -[07:36:18] WARNING: no name column found on line 56 -[07:36:18] WARNING: no name column found on line 57 -[07:36:18] WARNING: no name column found on line 58 -[07:36:18] WARNING: no name column found on line 59 -[07:36:18] WARNING: no name column found on line 60 -[07:36:18] WARNING: no name column found on line 61 -[07:36:18] WARNING: no name column found on line 62 -[07:36:18] WARNING: no name column found on line 63 -[07:36:18] WARNING: no name column found on line 64 -[07:36:18] WARNING: no name column found on line 65 -[07:36:18] WARNING: no name column found on line 66 -[07:36:18] WARNING: no name column found on line 67 -[07:36:18] WARNING: no name column found on line 68 -[07:36:18] WARNING: no name column found on line 69 -[07:36:18] WARNING: no name column found on line 70 -[07:36:18] WARNING: no name column found on line 71 -[07:36:18] WARNING: no name column found on line 72 -[07:36:18] WARNING: no name column found on line 73 -[07:36:18] WARNING: no name column found on line 74 -[07:36:18] WARNING: no name column found on line 75 -[07:36:18] WARNING: no name column found on line 76 -[07:36:18] WARNING: no name column found on line 77 -[07:36:18] WARNING: no name column found on line 78 -[07:36:18] WARNING: no name column found on line 79 -[07:36:18] WARNING: no name column found on line 80 -[07:36:18] WARNING: no name column found on line 81 -[07:36:18] WARNING: no name column found on line 82 -[07:36:18] WARNING: no name column found on line 83 -[07:36:18] WARNING: no name column found on line 84 -[07:36:18] WARNING: no name column found on line 85 -[07:36:18] WARNING: no name column found on line 86 -[07:36:18] WARNING: no name column found on line 87 -[07:36:18] WARNING: no name column found on line 88 -[07:36:18] WARNING: no name column found on line 89 -[07:36:18] WARNING: no name column found on line 90 -[07:36:18] WARNING: no name column found on line 91 -[07:36:18] WARNING: no name column found on line 92 -[07:36:18] WARNING: no name column found on line 93 -[07:36:18] WARNING: no name column found on line 94 -[07:36:18] WARNING: no name column found on line 95 -[07:36:18] WARNING: no name column found on line 96 -[07:36:18] WARNING: no name column found on line 97 -[07:36:18] WARNING: no name column found on line 98 -[07:36:18] WARNING: no name column found on line 99 -[07:36:18] WARNING: no name column found on line 100 -[07:36:18] WARNING: no name column found on line 101 -[07:36:18] WARNING: no name column found on line 102 -[07:36:18] WARNING: no name column found on line 103 -[07:36:18] WARNING: no name column found on line 104 -[07:36:18] WARNING: no name column found on line 105 -[07:36:18] WARNING: no name column found on line 106 -[07:36:18] WARNING: no name column found on line 107 -[07:36:18] WARNING: no name column found on line 108 -[07:36:18] WARNING: no name column found on line 109 -[07:36:18] WARNING: no name column found on line 110 -[07:36:18] WARNING: no name column found on line 111 -[07:36:18] WARNING: no name column found on line 112 -[07:36:18] WARNING: no name column found on line 113 -[07:36:18] WARNING: no name column found on line 114 -[07:36:18] WARNING: no name column found on line 115 -[07:36:18] WARNING: no name column found on line 116 -[07:36:18] WARNING: no name column found on line 117 -[07:36:18] WARNING: no name column found on line 118 -[07:36:18] WARNING: no name column found on line 119 -[07:36:18] WARNING: no name column found on line 120 -[07:36:18] WARNING: no name column found on line 121 -[07:36:18] WARNING: no name column found on line 122 -[07:36:18] WARNING: no name column found on line 123 -[07:36:18] WARNING: no name column found on line 124 -[07:36:18] WARNING: no name column found on line 125 -[07:36:18] WARNING: no name column found on line 126 -[07:36:18] WARNING: no name column found on line 127 -[07:36:18] WARNING: no name column found on line 128 -[07:36:18] WARNING: no name column found on line 129 -[07:36:18] WARNING: no name column found on line 130 -[07:36:18] WARNING: no name column found on line 131 -[07:36:18] WARNING: no name column found on line 132 -[07:36:18] WARNING: no name column found on line 133 -[07:36:18] WARNING: no name column found on line 134 -[07:36:18] WARNING: no name column found on line 135 -[07:36:18] WARNING: no name column found on line 136 -[07:36:18] WARNING: no name column found on line 137 -[07:36:18] WARNING: no name column found on line 138 -[07:36:18] WARNING: no name column found on line 139 -[07:36:18] WARNING: no name column found on line 140 -[07:36:18] WARNING: no name column found on line 141 -[07:36:18] WARNING: no name column found on line 142 -[07:36:18] WARNING: no name column found on line 143 -[07:36:18] WARNING: no name column found on line 144 -[07:36:18] WARNING: no name column found on line 145 -[07:36:18] WARNING: no name column found on line 146 -[07:36:18] WARNING: no name column found on line 147 -[07:36:18] WARNING: no name column found on line 148 -[07:36:18] WARNING: no name column found on line 149 -[07:36:18] WARNING: no name column found on line 150 -[07:36:18] WARNING: no name column found on line 151 -[07:36:18] WARNING: no name column found on line 152 -[07:36:18] WARNING: no name column found on line 153 -[07:36:18] WARNING: no name column found on line 154 -[07:36:18] WARNING: no name column found on line 155 -[07:36:18] WARNING: no name column found on line 156 -[07:36:18] WARNING: no name column found on line 157 -[07:36:18] WARNING: no name column found on line 158 -[07:36:18] WARNING: no name column found on line 159 -[07:36:18] WARNING: no name column found on line 160 -[07:36:18] WARNING: no name column found on line 161 -[07:36:18] WARNING: no name column found on line 162 -[07:36:18] WARNING: no name column found on line 163 -[07:36:18] WARNING: no name column found on line 164 -[07:36:18] WARNING: no name column found on line 165 -[07:36:18] WARNING: no name column found on line 166 -[07:36:18] WARNING: no name column found on line 167 -[07:36:18] WARNING: no name column found on line 168 -[07:36:18] WARNING: no name column found on line 169 -[07:36:18] WARNING: no name column found on line 170 -[07:36:18] WARNING: no name column found on line 171 -[07:36:18] WARNING: no name column found on line 172 -[07:36:18] WARNING: no name column found on line 173 -[07:36:18] WARNING: no name column found on line 174 -[07:36:18] WARNING: no name column found on line 175 -[07:36:18] WARNING: no name column found on line 176 -[07:36:18] WARNING: no name column found on line 177 -[07:36:18] WARNING: no name column found on line 178 -[07:36:18] WARNING: no name column found on line 179 -[07:36:18] WARNING: no name column found on line 180 -[07:36:18] WARNING: no name column found on line 181 -[07:36:18] WARNING: no name column found on line 182 -[07:36:18] WARNING: no name column found on line 183 -[07:36:18] WARNING: no name column found on line 184 -[07:36:18] WARNING: no name column found on line 185 -[07:36:18] WARNING: no name column found on line 186 -[07:36:18] WARNING: no name column found on line 187 -[07:36:18] WARNING: no name column found on line 188 -[07:36:18] WARNING: no name column found on line 189 -[07:36:18] WARNING: no name column found on line 190 -[07:36:18] WARNING: no name column found on line 191 -[07:36:18] WARNING: no name column found on line 192 -[07:36:18] WARNING: no name column found on line 193 -[07:36:18] WARNING: no name column found on line 194 -[07:36:18] WARNING: no name column found on line 195 -[07:36:18] WARNING: no name column found on line 196 -[07:36:18] WARNING: no name column found on line 197 -[07:36:18] WARNING: no name column found on line 198 -[07:36:18] WARNING: no name column found on line 199 -[07:36:18] WARNING: no name column found on line 200 -[07:36:18] WARNING: no name column found on line 201 -[07:36:18] WARNING: no name column found on line 202 -[07:36:18] WARNING: no name column found on line 203 -[07:36:18] WARNING: no name column found on line 204 -[07:36:18] WARNING: no name column found on line 205 -[07:36:18] WARNING: no name column found on line 206 -[07:36:18] WARNING: no name column found on line 207 -[07:36:18] WARNING: no name column found on line 208 -[07:36:18] WARNING: no name column found on line 209 -[07:36:18] WARNING: no name column found on line 210 -[07:36:18] WARNING: no name column found on line 211 -[07:36:18] WARNING: no name column found on line 212 -[07:36:18] WARNING: no name column found on line 213 -[07:36:18] WARNING: no name column found on line 214 -[07:36:18] WARNING: no name column found on line 215 -[07:36:18] WARNING: no name column found on line 216 +..[04:09:02] WARNING: not removing hydrogen atom without neighbors +.[04:09:02] WARNING: not removing hydrogen atom without neighbors +.[04:09:02] WARNING: no name column found on line 1 +[04:09:02] WARNING: no name column found on line 2 +[04:09:02] WARNING: no name column found on line 3 +[04:09:02] WARNING: no name column found on line 4 +[04:09:02] WARNING: no name column found on line 5 +[04:09:02] WARNING: no name column found on line 6 +[04:09:02] WARNING: no name column found on line 7 +[04:09:02] WARNING: no name column found on line 8 +[04:09:02] WARNING: no name column found on line 9 +[04:09:02] WARNING: no name column found on line 10 +[04:09:02] WARNING: no name column found on line 11 +[04:09:02] WARNING: no name column found on line 12 +[04:09:02] WARNING: no name column found on line 13 +[04:09:02] WARNING: no name column found on line 14 +[04:09:02] WARNING: no name column found on line 15 +[04:09:02] WARNING: no name column found on line 16 +[04:09:02] WARNING: no name column found on line 17 +[04:09:02] WARNING: no name column found on line 18 +[04:09:02] WARNING: no name column found on line 19 +[04:09:02] WARNING: no name column found on line 20 +[04:09:02] WARNING: no name column found on line 21 +[04:09:02] WARNING: no name column found on line 22 +[04:09:02] WARNING: no name column found on line 23 +[04:09:02] WARNING: no name column found on line 24 +[04:09:02] WARNING: no name column found on line 25 +[04:09:02] WARNING: no name column found on line 26 +[04:09:02] WARNING: no name column found on line 27 +[04:09:02] WARNING: no name column found on line 28 +[04:09:02] WARNING: no name column found on line 29 +[04:09:02] WARNING: no name column found on line 30 +[04:09:02] WARNING: no name column found on line 31 +[04:09:02] WARNING: no name column found on line 32 +[04:09:02] WARNING: no name column found on line 33 +[04:09:02] WARNING: no name column found on line 34 +[04:09:02] WARNING: no name column found on line 35 +[04:09:02] WARNING: no name column found on line 36 +[04:09:02] WARNING: no name column found on line 37 +[04:09:02] WARNING: no name column found on line 38 +[04:09:02] WARNING: no name column found on line 39 +[04:09:02] WARNING: no name column found on line 40 +[04:09:02] WARNING: no name column found on line 41 +[04:09:02] WARNING: no name column found on line 42 +[04:09:02] WARNING: no name column found on line 43 +[04:09:02] WARNING: no name column found on line 44 +[04:09:02] WARNING: no name column found on line 45 +[04:09:02] WARNING: no name column found on line 46 +[04:09:02] WARNING: no name column found on line 47 +[04:09:02] WARNING: no name column found on line 48 +[04:09:02] WARNING: no name column found on line 49 +[04:09:02] WARNING: no name column found on line 50 +[04:09:02] WARNING: no name column found on line 51 +[04:09:02] WARNING: no name column found on line 52 +[04:09:02] WARNING: no name column found on line 53 +[04:09:02] WARNING: no name column found on line 54 +[04:09:02] WARNING: no name column found on line 55 +[04:09:02] WARNING: no name column found on line 56 +[04:09:02] WARNING: no name column found on line 57 +[04:09:02] WARNING: no name column found on line 58 +[04:09:02] WARNING: no name column found on line 59 +[04:09:02] WARNING: no name column found on line 60 +[04:09:02] WARNING: no name column found on line 61 +[04:09:02] WARNING: no name column found on line 62 +[04:09:02] WARNING: no name column found on line 63 +[04:09:02] WARNING: no name column found on line 64 +[04:09:02] WARNING: no name column found on line 65 +[04:09:02] WARNING: no name column found on line 66 +[04:09:02] WARNING: no name column found on line 67 +[04:09:02] WARNING: no name column found on line 68 +[04:09:02] WARNING: no name column found on line 69 +[04:09:02] WARNING: no name column found on line 70 +[04:09:02] WARNING: no name column found on line 71 +[04:09:02] WARNING: no name column found on line 72 +[04:09:02] WARNING: no name column found on line 73 +[04:09:02] WARNING: no name column found on line 74 +[04:09:02] WARNING: no name column found on line 75 +[04:09:02] WARNING: no name column found on line 76 +[04:09:02] WARNING: no name column found on line 77 +[04:09:02] WARNING: no name column found on line 78 +[04:09:02] WARNING: no name column found on line 79 +[04:09:02] WARNING: no name column found on line 80 +[04:09:02] WARNING: no name column found on line 81 +[04:09:02] WARNING: no name column found on line 82 +[04:09:02] WARNING: no name column found on line 83 +[04:09:02] WARNING: no name column found on line 84 +[04:09:02] WARNING: no name column found on line 85 +[04:09:02] WARNING: no name column found on line 86 +[04:09:02] WARNING: no name column found on line 87 +[04:09:02] WARNING: no name column found on line 88 +[04:09:02] WARNING: no name column found on line 89 +[04:09:02] WARNING: no name column found on line 90 +[04:09:02] WARNING: no name column found on line 91 +[04:09:02] WARNING: no name column found on line 92 +[04:09:02] WARNING: no name column found on line 93 +[04:09:02] WARNING: no name column found on line 94 +[04:09:02] WARNING: no name column found on line 95 +[04:09:02] WARNING: no name column found on line 96 +[04:09:02] WARNING: no name column found on line 97 +[04:09:02] WARNING: no name column found on line 98 +[04:09:02] WARNING: no name column found on line 99 +[04:09:02] WARNING: no name column found on line 100 +[04:09:02] WARNING: no name column found on line 101 +[04:09:02] WARNING: no name column found on line 102 +[04:09:02] WARNING: no name column found on line 103 +[04:09:02] WARNING: no name column found on line 104 +[04:09:02] WARNING: no name column found on line 105 +[04:09:02] WARNING: no name column found on line 106 +[04:09:02] WARNING: no name column found on line 107 +[04:09:02] WARNING: no name column found on line 108 +[04:09:02] WARNING: no name column found on line 109 +[04:09:02] WARNING: no name column found on line 110 +[04:09:02] WARNING: no name column found on line 111 +[04:09:02] WARNING: no name column found on line 112 +[04:09:02] WARNING: no name column found on line 113 +[04:09:02] WARNING: no name column found on line 114 +[04:09:02] WARNING: no name column found on line 115 +[04:09:02] WARNING: no name column found on line 116 +[04:09:02] WARNING: no name column found on line 117 +[04:09:02] WARNING: no name column found on line 118 +[04:09:02] WARNING: no name column found on line 119 +[04:09:02] WARNING: no name column found on line 120 +[04:09:02] WARNING: no name column found on line 121 +[04:09:02] WARNING: no name column found on line 122 +[04:09:02] WARNING: no name column found on line 123 +[04:09:02] WARNING: no name column found on line 124 +[04:09:02] WARNING: no name column found on line 125 +[04:09:02] WARNING: no name column found on line 126 +[04:09:02] WARNING: no name column found on line 127 +[04:09:02] WARNING: no name column found on line 128 +[04:09:02] WARNING: no name column found on line 129 +[04:09:02] WARNING: no name column found on line 130 +[04:09:02] WARNING: no name column found on line 131 +[04:09:02] WARNING: no name column found on line 132 +[04:09:02] WARNING: no name column found on line 133 +[04:09:02] WARNING: no name column found on line 134 +[04:09:02] WARNING: no name column found on line 135 +[04:09:02] WARNING: no name column found on line 136 +[04:09:02] WARNING: no name column found on line 137 +[04:09:02] WARNING: no name column found on line 138 +[04:09:02] WARNING: no name column found on line 139 +[04:09:02] WARNING: no name column found on line 140 +[04:09:02] WARNING: no name column found on line 141 +[04:09:02] WARNING: no name column found on line 142 +[04:09:02] WARNING: no name column found on line 143 +[04:09:02] WARNING: no name column found on line 144 +[04:09:02] WARNING: no name column found on line 145 +[04:09:02] WARNING: no name column found on line 146 +[04:09:02] WARNING: no name column found on line 147 +[04:09:02] WARNING: no name column found on line 148 +[04:09:02] WARNING: no name column found on line 149 +[04:09:02] WARNING: no name column found on line 150 +[04:09:02] WARNING: no name column found on line 151 +[04:09:02] WARNING: no name column found on line 152 +[04:09:02] WARNING: no name column found on line 153 +[04:09:02] WARNING: no name column found on line 154 +[04:09:02] WARNING: no name column found on line 155 +[04:09:02] WARNING: no name column found on line 156 +[04:09:02] WARNING: no name column found on line 157 +[04:09:02] WARNING: no name column found on line 158 +[04:09:02] WARNING: no name column found on line 159 +[04:09:02] WARNING: no name column found on line 160 +[04:09:02] WARNING: no name column found on line 161 +[04:09:02] WARNING: no name column found on line 162 +[04:09:02] WARNING: no name column found on line 163 +[04:09:02] WARNING: no name column found on line 164 +[04:09:02] WARNING: no name column found on line 165 +[04:09:02] WARNING: no name column found on line 166 +[04:09:02] WARNING: no name column found on line 167 +[04:09:02] WARNING: no name column found on line 168 +[04:09:02] WARNING: no name column found on line 169 +[04:09:02] WARNING: no name column found on line 170 +[04:09:02] WARNING: no name column found on line 171 +[04:09:02] WARNING: no name column found on line 172 +[04:09:02] WARNING: no name column found on line 173 +[04:09:02] WARNING: no name column found on line 174 +[04:09:02] WARNING: no name column found on line 175 +[04:09:02] WARNING: no name column found on line 176 +[04:09:02] WARNING: no name column found on line 177 +[04:09:02] WARNING: no name column found on line 178 +[04:09:02] WARNING: no name column found on line 179 +[04:09:02] WARNING: no name column found on line 180 +[04:09:02] WARNING: no name column found on line 181 +[04:09:02] WARNING: no name column found on line 182 +[04:09:02] WARNING: no name column found on line 183 +[04:09:02] WARNING: no name column found on line 184 +[04:09:02] WARNING: no name column found on line 185 +[04:09:02] WARNING: no name column found on line 186 +[04:09:02] WARNING: no name column found on line 187 +[04:09:02] WARNING: no name column found on line 188 +[04:09:02] WARNING: no name column found on line 189 +[04:09:02] WARNING: no name column found on line 190 +[04:09:02] WARNING: no name column found on line 191 +[04:09:02] WARNING: no name column found on line 192 +[04:09:02] WARNING: no name column found on line 193 +[04:09:02] WARNING: no name column found on line 194 +[04:09:02] WARNING: no name column found on line 195 +[04:09:02] WARNING: no name column found on line 196 +[04:09:02] WARNING: no name column found on line 197 +[04:09:02] WARNING: no name column found on line 198 +[04:09:02] WARNING: no name column found on line 199 +[04:09:02] WARNING: no name column found on line 200 +[04:09:02] WARNING: no name column found on line 201 +[04:09:02] WARNING: no name column found on line 202 +[04:09:02] WARNING: no name column found on line 203 +[04:09:02] WARNING: no name column found on line 204 +[04:09:02] WARNING: no name column found on line 205 +[04:09:02] WARNING: no name column found on line 206 +[04:09:02] WARNING: no name column found on line 207 +[04:09:02] WARNING: no name column found on line 208 +[04:09:02] WARNING: no name column found on line 209 +[04:09:02] WARNING: no name column found on line 210 +[04:09:02] WARNING: no name column found on line 211 +[04:09:02] WARNING: no name column found on line 212 +[04:09:02] WARNING: no name column found on line 213 +[04:09:02] WARNING: no name column found on line 214 +[04:09:02] WARNING: no name column found on line 215 +[04:09:02] WARNING: no name column found on line 216 ...... ---------------------------------------------------------------------- -Ran 10 tests in 0.162s +Ran 10 tests in 0.197s OK .................. ---------------------------------------------------------------------- -Ran 18 tests in 0.901s +Ran 18 tests in 2.259s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.068s +Ran 3 tests in 0.178s OK ........ ---------------------------------------------------------------------- -Ran 8 tests in 0.029s +Ran 8 tests in 0.105s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.015s +Ran 2 tests in 0.052s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.017s +Ran 2 tests in 0.041s OK . ---------------------------------------------------------------------- -Ran 1 test in 0.088s +Ran 1 test in 0.100s OK ........ ---------------------------------------------------------------------- -Ran 8 tests in 0.002s +Ran 8 tests in 0.003s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.006s +Ran 3 tests in 0.008s OK ... @@ -28862,27 +28893,27 @@ OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.005s +Ran 4 tests in 0.006s OK ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.014s +Ran 7 tests in 0.030s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.021s +Ran 4 tests in 0.077s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 3.014s +Ran 4 tests in 6.949s OK .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.052s +Ran 10 tests in 0.151s OK . @@ -28892,29 +28923,29 @@ OK .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.006s +Ran 10 tests in 0.016s OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.078s +Ran 5 tests in 0.120s OK -.........[07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -[07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -[07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -[07:36:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -.......[07:36:36] Molecule does not have explicit Hs. Consider calling AddHs() -[07:36:36] Molecule does not have explicit Hs. Consider calling AddHs() +.........[04:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +[04:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +[04:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +[04:09:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +.......[04:09:46] Molecule does not have explicit Hs. Consider calling AddHs() +[04:09:46] Molecule does not have explicit Hs. Consider calling AddHs() ..... ---------------------------------------------------------------------- -Ran 21 tests in 5.392s +Ran 21 tests in 10.379s OK mol_197 219.10,35.89,110.98,11.56,110.32,11.04,95.23,10.25,0.00 mol_223 -243.67,7.40,134.64,0.81,134.56,0.81,85.50,0.37,0.00 +243.69,7.30,134.82,1.04,134.75,1.04,85.57,0.33,0.00 mol_269 216.26,5.67,105.00,0.87,103.81,0.89,89.27,0.92,6.00 . @@ -28922,7 +28953,7 @@ Ran 1 test in 0.000s OK -...[07:36:37] +...[04:09:48] **** Pre-condition Violation @@ -28933,63 +28964,63 @@ . ---------------------------------------------------------------------- -Ran 4 tests in 0.013s +Ran 4 tests in 0.029s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 6.519s +Ran 2 tests in 21.410s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.111s +Ran 2 tests in 0.416s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.014s +Ran 3 tests in 0.030s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.021s +Ran 4 tests in 0.031s OK -.....[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors -[07:36:46] WARNING: not removing hydrogen atom without neighbors +.....[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors +[04:10:17] WARNING: not removing hydrogen atom without neighbors ..... ---------------------------------------------------------------------- -Ran 10 tests in 0.350s +Ran 10 tests in 0.941s OK ssssss..........s/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu/rdkit/Chem/Draw/__init__.py:237: DeprecationWarning: legacy DrawingOptions not translated for new drawing code, please update manually warnings.warn( ..... ---------------------------------------------------------------------- -Ran 22 tests in 4.573s +Ran 22 tests in 13.409s OK (skipped=7) sss. ---------------------------------------------------------------------- -Ran 4 tests in 0.522s +Ran 4 tests in 0.748s OK (skipped=3) ssss @@ -28999,43 +29030,47 @@ OK (skipped=4) .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.827s +Ran 10 tests in 1.107s OK -...[07:36:55] SMARTS Parse Error: syntax error while parsing: boromicacid -[07:36:55] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -[07:36:55] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -[07:36:55] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -[07:36:55] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -[07:36:55] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -[07:36:55] reaction has no reactants -[07:36:55] reaction has no products -[07:36:55] initialization failed -[07:36:55] reaction has no reactants -[07:36:55] reaction has no products +...[04:10:41] SMARTS Parse Error: syntax error while parsing: boromicacid +[04:10:41] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +[04:10:41] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +[04:10:41] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +[04:10:41] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +[04:10:41] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +[04:10:41] reaction has no reactants +[04:10:41] reaction has no products +[04:10:41] initialization failed +[04:10:41] reaction has no reactants +[04:10:41] reaction has no products . ---------------------------------------------------------------------- -Ran 4 tests in 0.026s +Ran 4 tests in 0.049s OK ['C[C@@H](F)CN', 'C[C@@H](F)CN |a:1|', 'C[C@H](F)CN |o1:1|', 'C[C@H](F)CN |&1:1|'] .... ---------------------------------------------------------------------- -Ran 4 tests in 0.011s +Ran 4 tests in 0.018s OK ........................ ---------------------------------------------------------------------- -Ran 24 tests in 0.095s +Ran 24 tests in 0.168s OK !!! TEST FAILURE: python UnitTestInchi.py {} !!! TEST FAILURE: python UnitTestPandasTools.py {} +6: [04:13:36] Finished: testMultipleTimes() +6: [04:13:36] +6: ----------------------------------------- +223/223 Test #6: testConcurrentQueue .................... Passed 591.19 sec 99% tests passed, 3 tests failed out of 223 -Total Test time (real) = 119.31 sec +Total Test time (real) = 591.23 sec The following tests FAILED: 1 - testInchi (Subprocess aborted) @@ -29044,7 +29079,7 @@ Errors while running CTest make[2]: *** [Makefile:94: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' -dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 returned exit code 2 +dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20 returned exit code 2 make[1]: [debian/rules:134: override_dh_auto_test] Error 25 (ignored) make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' create-stamp debian/debhelper-build-stamp @@ -29054,7 +29089,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_auto_install - cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/rdkit-202309.3/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/rdkit-202309.3/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202309.3 -B/build/reproducible-path/rdkit-202309.3/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -29065,1397 +29100,1397 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DistanceGeometry +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DistanceGeometry/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/six.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Numerics +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Numerics/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemutils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemdraw_qax.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/retest.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/listutils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/comhack.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/cactvs.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemdraw.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/spiral.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/fileutils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt4.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/Fontmapping.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/pidPyart.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/pidSVG.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/colors.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/stringformat.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/pagesizes.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pidPDF.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfgen.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfgeom.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfdoc.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfutils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfmetrics.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/__pycache__/pstests.cpython-312.pyc +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/__pycache__/pidtest.cpython-312.pyc +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/pidtest.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/pstests.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/testallps.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/testallps.ps +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pidPIL.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/pid.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util/HTMLPiddler.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/pidWxDc.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/pidWX.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples/formatted-strings.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK/pidTK.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab/pidReportLab.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/utils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/psmetrics.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/pidPS.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/fontinfo.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/latin1MetricsCache.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Avalon +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Avalon/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Output.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Node.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Supply.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Transform.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SDSupply.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesSupply.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/demo.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/DbMolSupply.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Filter.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Geometry +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Geometry/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/RDLogger.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbConnection.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbInfo.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbModule.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbResultSet.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbReport.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/StorageUtils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbUtils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/RDConfig.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters/SimilarityPickers.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip/Metric +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip/Metric/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EnumerateHeterocycles.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/AtomTypes.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/Fingerprinter.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/EState_VSA.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/EState.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ShowMols.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/QED.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/SimilarityScreener.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/MolSimilarity.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/FingerprintMols.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/ClusterMols.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/DbFpSupplier.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/SigFactory.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Matcher.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/LazyGenerator.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Utils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/__pycache__ --- Installing: 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Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/PandasPatcher.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey/InchiInfo.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey/InchiInfo.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey/MolKey.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolSurf.py --- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb/FingerprintUtils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb/Loader.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolDb/Loader_orig.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/nbtests/ChEMBL_quinolones.tsv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Randomize.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Descriptors.py --- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MACCSkeys.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/SATIS.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemicalForceFields.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Graphs.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/PandasTools.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FunctionalGroups.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/SimilarityScreener.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/ClusterMols.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/MolSimilarity.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/FingerprintMols.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fingerprints/DbFpSupplier.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/__init__.py -- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Scaffolds/MurckoScaffold.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Scaffolds/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Scaffolds/ScaffoldNetwork.ipynb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Scaffolds/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/DescriptorUtilities.py +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolStandardize --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolStandardize/errors.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolStandardize/validations.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolStandardize/test_standardizer.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolStandardize/standardize.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolStandardize/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolStandardize/tautomer.py --- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/AlignDepict.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemUtils/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Features +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Features/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Features/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Features/ShowFeats.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Features/FeatDirUtilsRD.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/Fingerprinter.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/EState_VSA.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/AtomTypes.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/EState/EState.py +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/FeatMapPoint.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/FeatMaps.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/FeatMapParser.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatMaps/FeatMapUtils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/PyMol.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolSurf.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FragmentMatcher.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ShowMols.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Suppliers +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Suppliers/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Suppliers/DbMolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Suppliers/__init__.py +-- Installing: 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Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/DSViewer.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Utils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Matcher.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/SigFactory.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Generate.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Pharm2D/LazyGenerator.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/QED.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/fmcs +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/fmcs/fmcs.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/fmcs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/fmcs/fmcs +-- 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/BRICS.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FastSDMolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemicalFeatures.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/SpacialScore.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/AllChem.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Crippen.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ForceField +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ForceField/__init__.py +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/HierarchyVis.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/BitEnsemble.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/RDRandom.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/SimDivFilters/SimilarityPickers.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/TestRunner.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/AnalyzeComposite.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/BuildQuantTree.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/SigTree.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/Tree.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/QuantTree.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/DecTree.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/ID3.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/BuildSigTree.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/TreeUtils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/CrossValidate.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/Forest.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/PruneTree.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/randomtest.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/TreeVis.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/murtagh_test.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/ClusterVis.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Standardize.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Murtagh.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Clusters.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Resemblance.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/ClusterUtils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Butina.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/ScreenComposite.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/files.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/CompositeRun.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/BuildComposite.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/ClusterVis.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Standardize.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/murtagh_test.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Resemblance.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Clusters.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/EnrichPlot.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MLUtils --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MLUtils/VoteImg.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MLUtils/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/CompoundDescriptors.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/Descriptors.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/Parser.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Descriptors/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT/Risk.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MLUtils/VoteImg.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/ModelPackage --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/ModelPackage/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/ModelPackage/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/ModelPackage/Packager.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/ModelPackage/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/ModelPackage/PackageUtils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/ModelPackage/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/NaiveBayes --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/NaiveBayes/CrossValidate.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/NaiveBayes/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/NaiveBayes/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/NaiveBayes/ClassificationModel.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MatOps.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/BuildComposite.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Scoring --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Scoring/Scoring.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Scoring/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Scoring/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/GrowComposite.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Scoring/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Scoring/Scoring.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/ScreenComposite.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/QuantTree.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/TreeVis.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/CrossValidate.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/BuildSigTree.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/BuildQuantTree.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/ID3.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/randomtest.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/DecTree.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/Forest.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/SigTree.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/PruneTree.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/TreeUtils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/Tree.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT/Risk.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/SLT/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Composite --- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Composite/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/EnrichPlot.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/DataUtils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/FindQuantBounds.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Quantize.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/MLData.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Transforms.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Stats.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/SplitData.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/AnalyzeComposite.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/NaiveBayes +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/NaiveBayes/CrossValidate.py +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Neural +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Neural/CrossValidate.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Neural/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Neural/Network.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Neural/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Neural/Trainers.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Neural/ActFuncs.py +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util/HTMLPiddler.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples/formatted-strings.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py --- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/psmetrics.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/fontinfo.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/pidPS.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/latin1MetricsCache.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfgeom.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfdoc.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pidPDF.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfutils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfmetrics.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfgen.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK/pidTK.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/pid.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/stringformat.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt4.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/utils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/pagesizes.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/pidSVG.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/pidPyart.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/Fontmapping.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/README --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pidPIL.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/spiral.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/comhack.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/cactvs.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/retest.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemutils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/fileutils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemdraw_qax.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/listutils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemdraw.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/RDConfig.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/six.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Numerics --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Numerics/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Supply.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/demo.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesSupply.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/DbMolSupply.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SDSupply.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Transform.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Filter.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Output.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Node.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Geometry --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Geometry/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/TestRunner.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ForceField --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ForceField/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/CompositeRun.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Transforms.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Quantize.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/FindQuantBounds.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/SplitData.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/MLData.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/DataUtils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Stats.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Crippen.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/DTDs --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/rddata.sql +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/struchk -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/DTDs +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Salts.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Crippen.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/RDData.sqlt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/README.md -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/README.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Salts.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/rddata.sql --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/RD.css +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.inkscape.svg +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.lrg.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/wiki +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.ai +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_33.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_54.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_38.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_20.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_19.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_44.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_11.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_30.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_10.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_3.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_35.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_61.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_23.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_29.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_51.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_16.png +-- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_24.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_62.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_13.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_14.png +-- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_4.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_21.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_47.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_59.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/Overview.md --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedInC++.md -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/api-docs.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/Cookbook.rst -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedInPython.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/BackwardsIncompatibleChanges.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/conf.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im1.png --- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_3.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im0.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im0.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_11.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_6.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_5.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb2.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im4.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_charges.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp1.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/stereo_annotation.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molC.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb2.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_8.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im6.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond3.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_3_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_4.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_3.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/Cc1ccccc1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp3.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid_aligned.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mol_metadata1.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_38_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_7.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_3.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_29_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_3.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553_2.svg --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_8_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mfp2_bit872.svg -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/substruct_search_parameters1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_6.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_35_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_39_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molG.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/ary_group.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im0.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/indole1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.jpg +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im0.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_6.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp3.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_0.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553_2.svg +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im2.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_12.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_missing1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_11.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molB.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_atoms.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_crippen.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond2.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_annotation_1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im0.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_3.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/Cc1ccccc1.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553.svg --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_19_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_5.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im3.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im5.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp3.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_5.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mfp2_bit872.svg --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_3.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_missing1.png +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/chiral.mol -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/input.mol -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.smi +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.test.sdf --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/test_multi_colours.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/cdk2.sdf --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/invalid.mol -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/README.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/cdk2.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/test_multi_colours.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/AmideBond.rxn -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/MinimalFeatures.fdef --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/invalid.mol +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.train.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.sdf -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/s1p_chembldoc89753.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/AmideBond.rxn --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/Cartridge.md --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_17.png --- 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/terminology_jp.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/introduction_jp.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/index.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.ai --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.inkscape.svg --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/wiki --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.lrg.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/compounds.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/Overview.md -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/Frames.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/README --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.h --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/pbf.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/README --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/pzc --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/pzc/readme.md --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.html --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_rfrag.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_list.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/create_mmp_db.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/rfrag.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/search_mmp_db.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/mol_transform.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/indexing.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/rfrag.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/create_mmp_db.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/search_mmp_db.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_fragmented.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smiles_mol_trans.smi --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_output.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans_smarts.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym.csv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_default.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxratio.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_fragmented.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks_mol_trans.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_smarts_output.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mol_trans_output.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_smi.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs_smarts.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxratio.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_smart_output.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mol_trans_output.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smiles_mol_trans.smi -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_transfroms.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym_maxheavy.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_default.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs_smarts.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_smi_output.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_transfroms.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_smart_output.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample.smi --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/indexing.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CMakeLists.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_smarts_output.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_output.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_rfrag.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_list.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/MolVS +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/MolVS/molvs_cli.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/setup.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/requirements.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/pytest.ini +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/README.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test/test_freewilson.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_scaffold.mol +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810.smi +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_act.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/freewilson.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/Frames.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/fraggle.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/rdkit_tversky.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/atomcontrib.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/readme.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/final_fraggle_results.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query_fragmentation.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/ChEMBL_11265_actives.smi +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/fragmentation_tversky_out +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query.smi +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/cxn_tversky.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fastcluster.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered.tsv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/sdf2smi.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/cdk2.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/cdk2.smi --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.cpp --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test.cpp --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/CMakeLists.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/CMakeLists.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/testConformerParser.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/test_list.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/rdConformerParser.cpp --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test_list.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.h +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/IFG +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/IFG/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.h +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/pbf.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/npscorer.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/publicnp.model.gz -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/README.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/identifyReactants.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/utils.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/Examples_CalcLigRMSD.ipynb -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/README.md -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/5dpv_complex.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/JVE.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/1C9.png --- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1C9_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i23_1C9.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/6c83.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3w2c_N15.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i24_1C9.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3m11_AKI.pdb --- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/BEG_test.pdb -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/lig_crystal_aligned.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/JVE_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_1.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1C9_renamed.pdb -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dt0.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test/test_freewilson.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/pytest.ini --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/requirements.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/freewilson.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/README.md --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/setup.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_act.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_scaffold.mol --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810.smi --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/IFG --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/IFG/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/N15_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3w2c_N15.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/ChiralDescriptors.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/README.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/MolVS --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/MolVS/molvs_cli.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/identifyReactants.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/utils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/README.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Glare --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/rdkit_tversky.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/readme.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/atomcontrib.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/cxn_tversky.py --- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test.cpp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.h +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.cpp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/CMakeLists.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/testConformerParser.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/CMakeLists.txt +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/FilterSet_NIBR2019_wPubChemExamples.html -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100.csv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100_out.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/FilterSet_NIBR2019_wPubChemExamples.html --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100.csv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/filterExamples.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/SubstructureFilter_HitTriaging_wPubChemExamples.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/README.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/pzc +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/pzc/readme.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.html +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Glare +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/TestDbCLI.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/pubchem.200.sdf --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.sdf -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr_q1.mol -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.smi +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/pubchem.200.sdf -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Fingerprints.sqlt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Compounds.sqlt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Descriptors.sqlt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/loadErrors.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/AtomPairs.sqlt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Descriptors.sqlt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Compounds.sqlt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Fingerprints.sqlt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.2.smi -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.2.smi -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/CreateDb.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/moe_like.dsc --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/TestDbCLI.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/SearchDb.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts/create_deb_packages.sh --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts/FeatFinderCLI.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts/PythonFormat.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts/test.sh -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts/README.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts/FeatFinderCLI.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/README -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/license.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRDInchiLib.so.1.2023.09.3 @@ -30499,11 +30534,11 @@ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/ConcurrentQueue.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash_fwd.hpp --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/extensions.hpp -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/float_functions.hpp -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/hash_float.hpp --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/extensions.hpp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/float_functions.hpp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRDBoost.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRDBoost.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRDBoost.so @@ -31079,6 +31114,11 @@ make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_python3 -ppython3-rdkit I: dh_python3 fs:421: renaming rdBase.so to rdBase.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming DistGeom.so to DistGeom.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdGeometry.so to rdGeometry.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdAbbreviations.so to rdAbbreviations.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdChemReactions.so to rdChemReactions.cpython-312-x86_64-linux-gnu.so @@ -31120,16 +31160,11 @@ I: dh_python3 fs:421: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolStandardize.so to rdMolStandardize.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming DistGeom.so to DistGeom.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming rdForceField.so to rdForceField.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming Clustering.so to Clustering.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-312-x86_64-linux-gnu.so I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdGeometry.so to rdGeometry.cpython-312-x86_64-linux-gnu.so -I: dh_python3 fs:421: renaming rdForceField.so to rdForceField.cpython-312-x86_64-linux-gnu.so +I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-312-x86_64-linux-gnu.so dh_numpy3 -ppython3-rdkit make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' dh_installsystemduser -O--buildsystem=cmake @@ -31777,15 +31812,15 @@ diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake -dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined -dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined @@ -31794,11 +31829,11 @@ dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202309.3-7_amd64.deb'. dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202309.3-7_amd64.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202309.3-7_all.deb'. -dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202309.3-7_all.deb'. -dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202309.3-7_amd64.deb'. dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202309.3-7_amd64.deb'. -dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202309.3-7_amd64.deb'. dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202309.3-7_amd64.deb'. +dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202309.3-7_amd64.deb'. +dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202309.3-7_all.deb'. +dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202309.3-7_amd64.deb'. dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202309.3-7_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202309.3-7_amd64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202309.3-7_amd64.changes @@ -31807,12 +31842,14 @@ 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/1159142/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1159142/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/3055525 and its subdirectories -I: Current time: Mon Dec 8 07:39:18 -12 2025 -I: pbuilder-time-stamp: 1765222758 +I: removing directory /srv/workspace/pbuilder/1159142 and its subdirectories +I: Current time: Wed Nov 6 04:20:20 +14 2024 +I: pbuilder-time-stamp: 1730816420